It's the not-too-distant future, a time when internet technology has swept the world into the Network Age! Everyone carries around a portable communications deviced called a ""PET."" Each PET contains a unique personality program, or NetNavi, that freely navigates the CyberWorld. Lan, an enthusiastic 11-year-old, is introduced to his own, custom-build NetNavi, MegaMan. At first, Lan only wants to use MegaMan to play in cyber NetBattles against his friends' NetNavis. But when computer systems all over town begin to burst into flames, Lan and MegaMan team together to fight against a mysterious criminal syndicate that calls itself World Three!

A robotic cat seems to have its wired crossed as it clamps its jaw onto Dex's calf. Lan and Maylu visit him in the hospital, but are greeted by a less than welcome reception. Meanwhile, Mr. Wily unleashes an electronic rampage of malfunctioning merchandise on DenTech City. Just as Dex is released from the hospital, he's attacked again--this time by a robotic dog! The cyber-pooch escapes, but leads Lan and Maylu on a pursuit that ends on a subway train. Unfortunately, Count Zap and ElecMan have launched a nasty net attack that causes the train to go careening out of control! It's up to Lan and MegaMan to stop the speeding bullet train before it becomes the ""disaster express!""

A mysterious young girl named Yai transfers into Lan's 5th Grade class. Impressed by her incredible wealth, Lan and Dex unwittingly find themselves trapped on the prococious little girl's estate. All the while, Maddy (an agent for World Three) and her maniacal NetNavi, WackoMan, unleash a devastating computer virus that causes the traffic lights in DenTech City to go haywire, creating an enormous traffic jam throughout the city! Lan jacks his PET into a traffic signal control computer, and discovers that the traffic management center has been infected by a computer virus. Will Lan and MegaMan be able to stop the panic?!

An eccentric guest lecturer, Mr. Higsby, has come to Lan's school. But the lesson he wants to teach isn't on the cirriculum! The nutty professor is on a quest to ""acquire"" all rare BattleChips from those he deems unworthy. His target... Yai. Using his NetNavi, NumberMan, Higsby takes over the school's control system and locks Yai, Ms. Mari, Dex, and Maylu in their classroom, then stages a lopsided NetBattle to obtain his precious prizes. Locked outside, Lan must find a way to send MegaMan to the rescue... before it's too late!

At the command of My. Wily, the evil leader of World Three, Maddy, Mr. Match and Count Zap unleash an aquarium full of robotic fish using a unique, jellyfish-type of computer virus. The robot-fish create utter chaos throughout DenTech City. MegaMan and Glide jack into the CyberMatrix to try and stop the virus, but soon find themselves in the path of a ferocious Tidal Wave Virus! Just as MegaMan and Glide are about to be swallowed by the enormous wave, a mysterious NetNavi called SharkMan appears... Is he friend, or foe?

All the water in DenTech City has dried up! World Three has captured Tory and his father Dr. Froid and forced them to use their NetNavi IceMan to freeze the programs that control DenTech City's Waterworks. Lan and his friends rush to save the day, but with MegaMan encased in ice and the Waterworks decaying, can they possibly stop World Three in time to restore the city's water?

World Three's Count Zap is on a robbing rampage, only no one knows that his real target is the videogame that AyanoTech is about to release; if he can steal that, he'll make kids all over the world miserable. Lan and his friends learn of the sinister plot, and MegaMan goes up against ElecMan to stop it. But even with the help from Black Rose and WoodMan, will MegaMan be able to stop the ultra-powerful ElecMan?

Feeling like he's lost his inner fire, Mr. Match decides the only way to ignite it again is by defeating MegaMan once and for all. To lure him into his high-temperature trap, Mr. Match sends TorchMan out on a spree of overheating chaos throughout DenTech City. Maylu happens to be at the salon at the time, her hair gets fried, and Lan makes the mistake of laughing at her. Meanwhile, MegaMan hasn't replied to TorchMan's mayhem, causing Mr. Match to grow impatient. He sends TorchMan to challenge MegaMan directly, but the message stops at Roll, who also happens to be mad at MegaMan! Maylu and Roll decide to take on TorchMan, falling right into the terrible trap. Will MegaMan show up before Roll gets toasted?

The wildly popular TV personality and Yoga master, Yahoot, is in cahoots with World Three! The menacing mystic uses his powerful NetNavi MagicMan to take over the airwaves and hypnotize the devoted viewing audience--turning the entire town into animals! MegaMan jacks in to confront MagicMan, but things get pretty tricky. Our hero is outmatched by the nasty Navi. Just when MegaMan is about to receive the final blow, ProtoMan, controlled by the mysterious champion NetBattler Chaud, comes to his defense, and takes down MagicMan!

Lan and his friends are excitedly training for the upcoming N1 Grand Prix. Unfortunately, the members of World Three have secretly signed up for the competition and Mr. Wily plans to unleash chaos and mayhem at the event. To make matters worse, Higsby's NetNavi, NumberMan, goes berserk while Higsby is trying to upgrade him. Lan and MegaMan rush to the rescue, but it takes them so long to neutralize NumberMan that they almost miss the NetBattle competition! Thanks to Yai and her private jet, Dex, GutsMan, Maylu, Roll, Lan, and MegaMan arrive at the N1 Grand Prix just in time. Dex and GutsMan make a grand entrance at the competition as Chaud issues a challenge to Lan and MegaMan.

The N1 Grand Prix is well under way and Lan's first match is full of surprises! His opponent turns out to be Miyu, the mysterious fortune teller. She uses her powers to predict Lan and MegaMan's every move! Miyu's Navi SkullMan seems unstoppable as he attacks MegaMan with blinding speed. It's going to take a bit more wit and an uncommon usage of BattleChips to beat this bonehead!!

Just before their Net Battle competition at the N1 Grand Prix, Maddy insults Maylu and Yai in the trendy Souvenir Shop. Maylu vows right then and there to beat Maddy and her NetNavi, WackoMan, in their upcoming match. Unfortunately, during the NetBattle, WackoMan proves that he's as much a cheater as Maddy. But just when it looks like Roll is going to be defeated, Maddy makes a critical mistake and Roll seizes the moment! Meanwhile, Lan and MegaMan take on Mr. Match and TorchMan. Like Maddy, Mr. Match hatches a diabolical scheme to trick Lan into losing the match. Will World Three succeed in defeating the best Navis in the N1 Grand Prix...?

The N1 Grand Prix rages on, and TorchMan and MegaMan are locked in a heated battle (continued from previous episode)... It seems like MegaMan has the upper hand when Mr. Match downloads a nasty virus to take control of the solar panels on the roof of the Floating Arena's dome. He mercilessly channels the sun's rays into a beam that showers agonizing heat down upon Lan. As MegaMan and Lan suffer the scorching onslaught, Dex, Yai, and Tory jack in their NetNavis to vanquish the viruses one by one. Just as MegaMan's about to become toast, the gang clears the last of the viruses. The Dome opens up, and Lan and MegaMan turn in a blazing victory. Higsby and NumberMan fight the last battle of the day against sweet Sal and WoodMan. Thinking that they can easily defeat the flower girl, Higsby and NumberMan receive an ego smashing as Sal and WoodMan take them out in one blow!

It's time to party! Lan and the gang did so well in their first week in the N1 Grand Prix that Yai invites everyone to a fancy restaurant to celebrate. But when our heroes get to the restaurant, someone is sitting at the table reserved for Yai's family. It's Chaud! Pompous and condescending, it doesn't take long before Chaud insults Yai's family as well as Lan's NetBattling skills. Lan, defending his and Yai's honor, follows Chaud out of the restauraunt and into the night, where he challenges him to a NetBattle. Just as the battle begins, World Three unleashes a hoarde of viruses programmed to delete both MegaMan and Chaud's NetNavi, ProtoMan!

After his brutal battle with Chaud, Lan knows that the only way MegaMan will ever have a chance against ProtoMan is to master the legendary Program Advance technique. Lan recruits Dex to help him as they launch into an impromptu, intensive training course. Meanwhile, WhaleMan and SharkMan are going at it in the main Dome. To give Lan more training time before his upcoming match, Commander Beef holds out until the last possible second before unleashing SharkMan's devastating offense. Lan still can't seem to get it right, but the show must go on. In a ferocious fight with Yahoot and MagicMan, Lan tries the Program Advance once more, this time with better results. He wins the match, but just barely. Chaud and ProtoMan are up next against Count Zap and ElecMan. The World Three nasties pull a cheap trick, but Chaud and ProtoMan tap into the full power of the Program Advance and delete the cheaters from the competition!

Schoolmates Maylu and Tory, with their NetNavis, Roll and IceMan, battle it out in Week Two of the N1 Grand Prix! After Roll defeats IceMan, the games shift to a more challenging event: the Tag Team Matches, as pairs of NetNavis battle each other. First up, the mysterious StoneMan and BlasterMan challenge GutsMan and WoodMan. By the end of the match, it's revealed that StoneMan and BlasterMan are actually Mr. Wily's secret weapons. The two are revealed to be Solo NetNavis, which means they have free will and can battle without NetOps! After soundly defeating GutsMan and WoodMan, the two Solo NetNavis set their sights on MegaMan and SharkMan! With the undefeated StoneMan and BlasterMan at his side, will Mr. Wily succeed in finding the NetNavi with the Ultimate Program?

2 on 2 battles continue: MegaMan and SharkMan (Commander Beef) vs. StoneMan and BlasterMan. StoneMan and BlasterMan open a hole in the arena, and the four NetNavis are quickly sucked out of the ring and into a cyber world. They have 10 minutes to return to the ring, or they will be disqualified. Finally, MegaMan and BlasterMan return, and MegaMan is victorious. But Lan suspects that Commander Beef is Maysa in disguise.

The N1 Grand Prix moves into a special, second round of Tag Team competition when it is announced that two teams, which had previously been eliminated, can now re-enter the games. The two lucky teams are chosen by a computerized wildcard, but World Three rigs the competition so that Mr. Match and Maddy are selected, pitting TorchMan and WackoMan against MegaMan and Roll. Neither Lan nor Maylu are nervous about the match-ups since they have beaten these opponents before. However, both our heroes are in for a frightening surprise when World Three tricks Maylu into downloading a special BattleChip that transforms Roll into an evil NetNavi! The newly transformed ""Empress"" immediately launches a vicious attack against MegaMan. Will she succeed in finally deleting him?

Disguised as Higsby, Yahoot gives Maylu an evil BattleChip, which she uses in her team match with Lan--against Mr. Match and Maddy. This ""twisted chip"" has now taken over her PET and put Roll under the control of Count Zap and World Three! Every time Lan sends MegaMan into action, Roll, now calling herself Empress, steps in his path and attacks our blue hero! Finally the real Higsby appears and tells Maylu the secret to stopping Roll from her rage. With Roll back to normal, Lan and Maylu easily win the match. Up next, Chaud and ProtoMan are teamed up with a teen NetBattler and his singing NetNavi, ShiningMan--against WhaleMan and RocketMan. Not exactly team players, Chaud and ProtoMan take out their opponents and ShiningMan in one blow!

It's the semi-finals at the N1 Grand Prix and MegaMan and Lan are teamed up with ProtoMan and Chaud against the Solo NetNavis, StoneMan and BlasterMan. Before the match, Chaud gets stuck in an elevator with Yai, but makes it back to the arena just in time. As the match begins, MegaMan is temporarily taken out of the battle by ProtoMan who then faces off against BlasterMan, and literally blows him away. MegaMan gets back in the action, but StoneMan buries him under a ton of viruses. Barely missing a beat, Chaud sends ProtoMan in to finish the job and blows StoneMan to pieces. But StoneMan has a regenerative program that allows the brute to pull himself back together again! Lan tells Chaud to use the Program Advance, but Chaud can't because he lost two critical BattleChips while saving Yai in the elevator incident. MegaMan returns and he and Lan unleash the Program Advance, taking StoneMan down. Now, it's on to the finals, where MegaMan and ProtoMan face off for the title of N1 Grand Pri

The match begins. Chaud insists on working alone, so he takes on BlasterMan and StoneMan single-handedly. BlasterMan is deleted, but StoneMan has a regenerative core that makes him difficult to delete. However, ProtoMan becomes overcome when Chaud realizes he lost the chips needed for the Program Advance in the elevator shaft with Yai.

At long last the waiting is over! The Championship Battle of the N1 Grand Prix has finally arrived, and the contestants are Lan and Chaud with their NetNavis MegaMan and ProtoMan! But as the teams clash in a dramatic battle, they unleash so much power that the hydraulic support beams holding up the Floating Arena are damaged and the arena starts sinking! While the terrified crowd evacuates, the gang realizes that Lan and Chaud are continuing their heated battle--and both plan to battle to the end, even if it means going down with the arena! While the gang watches from afar, Lan and Chaud's NetBattle climaxes with a never-before-seen Double Advance! As the crowd cheers, the energy the titanic Double Advance unleashes a powerful and malevolent NetNavi from his secret tomb. PharaohMan is released back into the world!

PharaohMan has returned, and he's back with a vengeance! Mr. Wily sends an army of StoneMan and BlasterMan clones to capture the NetNavi, but PharaohMan has plans of his own. Meanwhile, Lan gets a shock: Chaud actually feels bad about MegaMan being deleted and offers to help him! But maybe MegaMan isn't gone after all, since Lan and his friends find strange data on their PET's. While they try to figure out how to rebuild MegaMan, PharaohMan, angry because he was imprisoned for twenty years and had his ""kingdom"" taken from him, uses the Cyber Network to cause disasters in the real world. And then, Lan's father shows up to help Lan and his friends--surely he can bring MegaMan back.

In order to revive MegaMan, his back-up frame must be retrieved from the SciLab network. However, PharaohMan has taken over the network and turned it into a barren desert wasteland. Roll and the other NetNavis jack-in to retrieve the frame, but PharaohMan intervenes.

The BlasterMan/StoneMan clones attack PharaohMan, but he escapes unscathed. Roll and the others are not so lucky and are turned to stone by PharaohMan. As this part of the Cyber Net begins to collapse, ProtoMan succeeds in saving MegaMan's frame. SharkMan, SkullMan, and WoodMan work at shutting down SciLab's main computer, while ProtoMan takes on PharaohMan single-handedly. Just when it seems ProtoMan will be deleted, MegaMan returns and the two NetNavis attack PharaohMan with the Double Program Advance. BlasterMan and StoneMan reappear and take the weakened PharaohMan to Mr. Wily at World Three Headquarters. MegaMan follows them but is immediately set upon by BlasterMan and StoneMan, so Lan engages MegaMan's new ability, StyleChange, which allows MegaMan to easily defeat the Solo NetNavis. In the end, Mr. Wily and PharaohMan's showdown of wills ends in the destruction of World Three Headquarters.

For placing second in the N1, Lan wins a trip around the world. He starts in the tropical Jawaiian islands, and his friends follow along for some fun in the sun. However, a ghost ship appears, capturing Maysa and Tory. The kids infiltrate the boat to rescue their friends.

The girls enter a contest to be just like Aki, a virtual pop singer. However, contestants go missing, so the boys dress as Aki to investigate the situation. A virus has infected Aki causing the mayhem, so MegaMan, GutsMan, and Iceman jack-in to rescue their idol.

Lan visits Netopia's Heaven City, but as soon as he arrives, his PET is stolen. After chasing the thieves down, he befriends a man named Raoul with NetNavi ThunderMan. Meanwhile, the mayor of Heaven City has plans to bulldoze Raoul's downtown home, but Lan agrees to help fight back. Meanwhile, Mr. Match arrives to Jawaii islands to have a rematch with Lan, but he arrives too late: Lan left Jawaii islands.

While in Brand City, Lan sees a purse he'd like to buy for his mother, but it's too expensive. He learns of an underground NetBattle game where he can win the purse, but it's really a trap set up by Ms. Millionaire to capture NetNavis for her own personal museum. Meanwhile, Mr. Match arrives to Netopia's Heaven City, but he's too late again: Lan left Netopia's Heaven City.

Lan's bus breaks down while driving through Kingland, so he visits a nearby mansion. It's actually the home of Count Zap who has been persuaded by his mother, Mama Zap, to get revenge on Lan for destroying the WWW. Count Zap traps Lan in a NetBattle where he's shocked every time MegaMan takes damage. Meanwhile, Mr. Match mistakes the planes and goes to country where everyone knows about curry.

Lan's last venture of his vacation is to try all kinds of different curry—his favorite food. WWW members Mr. Match, Maddy, Count Zap, and Yahoot reunite to trap Lan during his all-you-can-eat curry buffet, but Lan's own friends make a surprise turn to help take the WWW down.

Back home, Lan is introduced to NetCity, an online city for NetNavis to interact in. Meanwhile, a NetNavi named AirMan traps Yai in her bathroom and fills it with hot steam. MegaMan goes to stop the NetNavi who claims to be a member of Grave, a new net-crime syndicate.

A strange acid rain and viruses loom over NetCity, destroying it. MegaMan and co. jack-in to fend off the viruses, and they soon discover an underground factory that's the source of the mayhem. But when MegaMan goes to destroy it, he meets ShadowMan, an assassin NetNavi hired to delete him.

Mysteriously, Higsby has become very wealthy, and Yai's family has gone broke. Mr. Gauss is responsible, a member of Grave who is using MagnetMan to switch people's bank accounts around. Lan and Chaud investigate the situation, but Gauss escapes.

Sal takes the kids on a camping trip into Okudan Valley. There, she meets a childhood friend Dave. But Dave claims to be a Grave member who plans to use QuickMan to destroy the valley's dam. It turns out to be a bluff but CutMan, another Grave member, appears to finish the job.

A new air-conditioning penguin toy is introduced during a heat wave, but they're really being distributed by Grave. Soon, the penguins begin to blanket DenTech City under a sheet of ice. Lan manages to jack-in to NetCity and finds that FreezeMan is responsible for this mess. FreezeMan is defeated with the help of another new NetNavi named HeatMan.

The events of episodes 33 and 36 are recapped through the point-of-view of the WWW. This episode elaborates on the deletion of TorchMan to the hands of FreezeMan, and the rebirth of TorchMan in the form of HeatMan thanks to the efforts of the enigmatic man named Famous.

The five younger brothers of CutMan declare revenge against MegaMan for deleting their older brother. Luring MegaMan into a fake China Town district, they begin attacking with a barrage of origami warriors. ProtoMan appears and assists in the rescue of MegaMan.

Lan meets a boy named Whip, unaware that he's really the princess of Brightland, Princess Pride. ShadowMan targets Pride because her NetNavi, KnightMan, has a valuable virus protection program. Lan and MegaMan aid "Whip" in the battle against ShadowMan.

Tora, world-class NetChess Battling Champion and his NetNavi KingMan, have come to DenTech City to challenge Lan and MegaMan. Tora never plays for free though, and demands that whoever loses the NetBattle must give their NetNavi to the winner! Lan accepts the challenge, but soon realizes he has no idea how to play chess! Luckily, Maylu does and partners up with Lan. As the incredible battle nears its end, ShadowMan mysteriously appears on a mission to delete both KingMan and MegaMan!

All of the NetNavis in DenTech City are turning into cats! A freak electrical storm released a Cat Virus that's causing the transformations. To add to the confusion, Rush has somehow materialized in the human world. Dr. Hikari shows up to lend his help, and he reveals that if the Cat Virus isn't stopped soon, MegaMan and the others will remain cats forever! After sixty-foot-tall versions of Rush and the Cat Virus face off in the human world, MegaMan and the others are able to defeat the Cat Virus and give Dr. Hikari the data he needs to write a vaccine program. Everything goes back to normal--except that Rush can still appear in the human world. Will the vaccine work? And why is Rush now suddenly able to appear in the human world whenever he wants? What is going on?

Maddy is bored and restless since the disintigration of World Three, so she jumps on the offer to become Mr. Gauss's new executive assistant--despite protests from her old companions. Meanwhile, Commander Beef gets wind of a secret meeting for senior Grave officers which is to take place at Gauss's mansion. He, Lan, and the others crash Gauss's costume party, unaware that it is actually a ruse to lure them into his trap. When Gauss traps them in the basement of his mansion and begins flooding it, Lan tries to save himself and his friends by jacking into the net while fighting rising waters. In order to pull the plug on the rising water, MegaMan must battle MagnetMan. Watching the drama unfold, Maddy begins questioning Grave's ruthless and controlling methods and decides to aid Lan, lending WackoMan's support to MegaMan in a mad NetBattle against MagnetMan. In the end, Maddy realizes that she's happier back with her old friends--even if it means washing dishes back at #1 Curry!

Kyuta, a new student in Lan's class, is the son of famous baseball player Kyuma Hoshida, but he's depressed about having to move from his old town. To cheer him up, Lan and all of his friends in DenTech City invite him to a game of NetBaseball.

When her NetNavi KnightMan goes out of control and threatens BrightLand's cyber defense system, Princess Pride summons Lan for help. Lan, Maylu, Dex, Yai, and Tory arrive quickly on the scene, to discover KnightMan hacking away at BrightLand's protective Firewall--the country's primary protection against enemy invasion! MegaMan jacks in to restrain KnightMan, but soon discovers that one of Princess Pride's newest NetNavi subjects, MoltanicMan, is in fact the real traitor! It was he who hypnotized KnightMan, causing him to go berserk, as part of his plan to tear down BrightLand's defenses! With these defenses, his own country, DarkLand, can invade! Will Lan and MegaMan be able to stop the crafty MoltanicMan, before BrightLand is destroyed?!

All contact with NetNavis in DenTech City's moon station has been lost! While Commander Beef rockets to the moon to investigate, Lan and his friends are trying to learn more about the mysterious new ""ExtraCodes"" rumored to make NetNavis mightier than ever! Then Commander Beef encounters a dangerous new NetNavi, PlanetMan, who's trying to take over the moon. But before the Commander can react he's locked outside the lunar station with only two hours of air left! With Mr. Famous's help, Lan and his friends rush to the space center and beam MegaMan and GutsMan to the moon's cyber station to battle PlanetMan. But even with MegaMan now wielding an ExtraCode to get the amazing AquaCustom Style, will he be able to handle its awesome, energy-draining power?

Maddy, Count Zap, Mr. Match, and Yahoot have just learned that the genius of their missing leader, Mr. Wily, lives on in a data chip stored safely on a faraway island--and with it lives their dream of restoring World Three! Luckily, Lan and his friends learn of the plan at the last minute and race to try and stop them! But with victory still up for grabs, the mysterious Mr. Gauss enters the picture and takes the Wily chip for himself! With Lan in hot pursuit, Mr. Gauss flees, but not before revealing a shocking secret about Count Zap!

AyanoTech is hosting a NetMobile Grand Prix in NetCity! MegaMan and his friends, plus World Three and the Net Agents, all compete to see who has the fastest NetVehicle! But the winning car will have to be more than just speedy, because in this race, anything goes, including using BattleChips to sideline your opponents. It's all legal! And, as if driving under those conditions weren't tricky enough, the CutMan Brothers, who vowed to take revenge against MegaMan, join the race and create utter mayhem! In all the confusion, who will take the lead and win?!

The mysterious Bass floats over NetCity, watching as the Grave VirusBeast rampages on the loose, devouring NetNavis and growing in size! Even with ProtoMan's help, Lan and MegaMan are powerless to stop the Beast from swallowing their friends! Can anything be done to halt this monster before it consumes the entire cyber network? What role does the cryptic Bass have to play?!

No one knows what to make of the mysterious new NetNavi Bass, but everyone is intruiged when it seems that he alone can resist the CyberBeast that's slowly destroying the entire Cyber Network! What will he do with that kind of power? What does he want? And whose side is he on: MegaMan's? Grave's? Taking no chances, Kid Grave sends FreezeMan to delete Bass. Then Bass makes off with an unconscious MegaMan, launching Lan and his friends on a desparate search to find him. And worst of all: Mr. Wily has returned.

The Grave VirusBeast continues absorbing the internet. Lan and his friends team up with former WWW members to try and stop Grave. However, Mr. Gauss and MagnetMan intervene, and a strange bug left behind by Bass in MegaMan's system begins to consume him. Meanwhile, Bass attempts to absorb the VirusBeast, but is himself absorbed instead.

At last MegaMan comes face-to-face with the terrifying Grave VirusBeast that's devouring the entire cyber world... and unless it can be stopped, the network will be destroyed and Mr. Wily will control the world! But it's a losing battle: even AquaCustom Style MegaMan falls before the power of the VirusBeast and is infected with a bug! Then the incredible happens! MegaMan regenerates and emerges in a completely new style: BugStyle! But he gets further infected by the VirusBeast in the process, and now the unstoppable, rampaging monster that's triggering the end of everything is... MegaMan himself!

When a vacuum robot sucks up everyone's PETs, Yai and her friends are forced to explore the booby-trapped depths of the Ayano mansion in order to retrieve their stolen NetNavis. Yai's comical and clumsy maid Sakurako makes the excavation more difficult for the cast.

Maysa and Higsby have both fallen for Ms. Mari, but she's in love with Commander Beef! Higsby challenges the Commander and Maysa to a NetBattle to prove he is the true hero. Meanwhile, Yai and her family manage to build a fantastic stadium for the event in one night, and since Ribitta is stuck somewhere in the Himalayas on assignment, Sal is persuaded to be the announcer at the match. Higsby's up first, but he's so nervous, he loses immediately. Then Lan, NetBattling for Maysa, finally gets to take on his idol, Commander Beef. The love battle is on. Who will have the heart of the shy schoolteacher?

Dex's little brother, Chisao, comes for a visit and our heroes discover the siblings are nothing alike. Chisao attends Kindergarten for geniuses! Chisao idolizes Dex, believing that his big brother is the gang's mentor and leader. Dex begs his friends to play along, just until Chisao returns home to Netopia. Meanwhile, a new noodle restaurant opens up next door to #1 Curry, creating a bitter rivalry between Yahoot and Saburo, the noodle shop owner. Saburo tricks Chisao into helping him sabotage Yahoot's restaurant, and gives him a NetNavi with new powers that stuns even MegaMan! In an explosive NetBattle, Saburo's scheme is uncovered, but when the smoke clears, will Dex remain a hero in his little brother's eyes?

Lan and Chaud are about to have the NetBattle to end all NetBattles, only it ends before it can really start. Chaud is called away on business for his father, so he rushes off to get to a small company to finish a cutting edge new Ultimate Molecular Chip they were hired to create. Chaud soon finds himself doing chores at the company, helping perfect the Molecular Chip, fighting off a hostile takeover of the business, and even defeating the viruses and NetNavi that the company's assistant released after trying to steal the Molecular Chip! What's so great about this chip? What will it be used for? And why is Chaud cleaning bathrooms to help make sure it gets done?

Lan's father, Dr. Hikari, has started an incredible experiment, bridging the CyberWorld to reality! But when things go terribly wrong, and his father goes missing, Lan fears the worst! The key to the experiment, the Dimension Core, has drawn powerful Viruses to it, and now these monsters have materialized in the human world! Lan and his friends must battle these increasingly terrible life-sized Viruses, while MegaMan and the other NetNavis desparately look for a way to help them before it's too late!

Lan, Maylu and Chisao visit the Sci-Labs and witness Dr. Hikari's latest experiment in Dimensional Area technology—CrossFusion, the merger of a NetOp with his/her NetNavi, but the CrossFusion makes a NetOp lose his strength. However, the laboratory is attacked by real-world viruses and the Darkloid NetNavi SavageMan. Lan has no choice but to perform CrossFusion himself and stop SavageMan. After beating SavageMan, Lan passes out, but recovers a few seconds later.

When Lan wakes up and realizes that his battle with BeastMan and his CrossFusion with MegaMan weren't just a dream, he rushes to SciLab, which is still in shambles from the battle. Lan ends up walking off with a SynchroChip, and it's a good thing he does--ShadeMan starts deleting NetCity, and after MegaMan is unable to stop him, viruses start appearing in the Human World! It's up to Lan and MegaMan to CrossFuse and stop them, but ShadeMan still manages to come out on top. Using the data he stole from NetCity, he fashions a powerful fortress. From there, he plans to strike out at the Human World and drive everyone off the planet!

Raika and Lan are instructed to work together to investigate what's apparently a ghost that's robbing banks and corporations. Unable to get along with each other, they decide to work independently. When the ringleader behind the thefts turns out to be DesertMan (who can make himself invisible), MegaMan finds himself in big trouble and facing a tough NetBattle all alone. Meanwhile SearchMan, against Raika's orders, goes in to rescue MegaMan. Raika is shocked that SearchMan has disobeyed his orders. MegaMan gains a new DoubleSoul power, Search Soul, and with it, he defeats DesertMan.

ShadeMan, who's suspicious of the Mysterious Man, schemes to obtain the DarkChips on his own. Soon after, information on the DarkChips is leaked to Manuela, but when she investigates, she's blocked by a Dimensional Area that surrounds the Secret Warehouse Lab. CrossFusion MegaMan and CrossFusion ProtoMan break through the Dimensional Area's barrier, but they find their way to the chips is blocked by the fearsome GravityMan. Working together, our heroes defeat GravityMan, but they discover, as does ShadeMan, that getting a hold of the elusive DarkChips is much more difficult than they thought.

BubbleMan is convinced that he has the answer to defeating MegaMan: DoubleSoul. The only thing is, true friendship is the basis of DoubleSoul, and BubbleMan has no friends. None of the Darkloids are willing to work with him, so he goes off in search of a Navi that he can trick into becoming his friend. Only he has it all wrong, and thinks that in order to make friends he needs to take data from them. BubbleMan finds SpoutMan and IceMan, and convinces them both to hang out with him, a first step to getting them to give him their allegiance. When MegaMan and the other encounter the odd trio, BubbleMan tricks SpoutMan and IceMan into battling their own friends!

Chaud is having trouble dealing with the loss of ProtoMan to darkness, but Lan helps comfort him with his loss. Later, when GravityMan and ProtoMan attack, Chaud is forced to fight against his own NetNavi to protect important NetSaver data while Lan handles GravityMan.

When MegaMan rescues SpoutMan from a Darkloid attack, SpoutMan begins idolizing his new hero and following him everywhere, causing Roll to grow jealous. Meanwhile, BurnerMan attacks, and MegaMan must fight, but SpoutMan and Roll get in the way. In the end, BurnerMan is deleted when MegaMan uses SpoutSoul against the Darkloid.

Yai needs her friends' help again. An AyanoTech satellite has been covered in space debris, so Lan and co. board a space station built from junk to solve the problem. In the station's network, MegaMan meets JunkDataMan, the NetNavi responsible for the mess, and a misunderstanding leads to a battle between the two.

The NetAgents have returned to DenTech City, and Lan is shocked to learn that everyone already knew their identities were Sal, Miyu, and Maysa. Mr. Gauss also returns to town to make a deal with Ms. Yuri, but mistakening Ms. Mari for her, he holds her hostage. Commander Beef dashes to rescue his love from danger.

Lan meets Misaki, the first person to test CrossFusion. Misaki uses his NetNavi PrismMan to help in the capture of GravityMan. However, Misaki is overcome with his desire to CrossFuse, and Ms. Yuri uses his desires to lure him toward a trap. Meanwhile, Chaud assists Lan with the Battle Chip Gate to delete GravityMan using the Program Advance.

Misaki uses the power of a Dark SynchroChip to CrossFuse, but as a side-effect, his human heart is enriched with darkness. Captured by the NetSavers, they begin to heal him, but Ms. Yuri reinstitutes his darkness, causing him to escape. Lan battles with Misaki in CrossFusion, but the battle causes Lan's PET to be badly damaged.

Lan must use his own body in order to help rebuild MegaMan after his PET is damaged beyond repair. Meanwhile, Nebula sends NovaMan, BrightMan, SwordMan, and FridgeMan to attack various locations. In Lan's absence, Raika works with old friend Raoul to stop the invasion. BrightMan is deleted, and the others retreat.

Dr. Hikari finishes Lan's new PET, the PET II, which amplifies CrossFusion abilities, but the installation isn't completed. However, Dark ProtoMan infiltrates the Sci-Labs to destroy the PET (with MegaMan inside). Anetta takes the PET and Dark ProtoMan gives chase with Chaud close behind to rescue her. Chaud and Anetta work together to capture Dark ProtoMan, but NovaMan appears to finish the job. The installation in PET II is finally completed. Lan appears and, using the PET II, easily deletes NovaMan.

Lan becomes arrogant with his new PET II's powers, so Chaud and Raoul pose as afro wig-wearing villains to teach Lan a lesson. However, SwordMan appears to cause problems, and he overcomes ThunderMan in battle. MegaMan uses ThunderSoul to stop SwordMan.

Lan and his friends' NetNavis disappear in a tornado of wind, and they track them to Shiisaa Island. There, they meet Lily and her NetNavi WindBlastMan. Ms. Yuri also appears on the island, hoping to steal the data within an ancient relic. When SpikeMan disrupts the relic, a huge storm brews over the island, and using WindSoul MegaMan defeats Spikeman.

Lan and Chisao are leaving a theme park on a train when SparkMan attacks the train's network. Sal has been tailing the NetNavi and sends WoodMan in to help with MegaMan. In order to delete SparkMan, MegaMan and WoodMan combine their powers to create WoodSoul.

A Dimensional Area has appeared over a factory in Sharo, so Raika calls for Lan to help infiltrate it against his general's orders. Inside, they meet FridgeMan who is trying to steal minerals. Upon his defeat, Lan learns that Raika was mostly trying to rescue his pet dog that was trapped in the factory.

While Lan is away in Sharo, Chaud and Maylu work together to investigate the disappearance of NetNavis who participated in the N1 Grand Prix last year. They meet a robot named Allegro and also re-encounter Kid Grave, now being controlled by Bass. After causing so much trouble, Bass gets rid of Allegro by destroying his CPU, and rejects an offer by Dark ProtoMan to join Nebula.

After having a dream about performing CrossFusion, Maylu wishes to do so and protect Lan for a change. While on a date together at an amusement park, SwordMan attacks and Lan drops his SynchroChip. Maylu picks it up, determined to CrossFuse, but she fails. In the end, Lan saves her again, but their relationship has grown.

An elderly man named Tensuke wishes to better connect with his grandson who cares more about NetBattling, not Tensuke's love for tops. Lan and Maylu decide to help Tensuke perfect his NetBattling skills with NetNavi TopMan.

While on summer vacation, Lan and Maylu search around the world for a beetle and find themselves in ancient desert ruins. There, they find a magic lamp that summons MistMan, a NetNavi genie, but Ms. Yuri, SwordMan, and FridgeMan also seek the power of MistMan. In the end, MistMan is freed and helps MegaMan in deleting both SwordMan and FridgeMan.

When Maylu receives a new kitten, Rush feels neglected and runs away on the internet. He befriends a Maloko sheep virus, but BubbleMan is causing electrical interference throughout the city in hopes of reviving ShadeMan. Rush and the Maloko intervene.

Using Control X, the NetSavers plan to locate Dr. Regal's hidden space hideout. But to stop their plan, Nebula sends an army of previously-deleted Darkloids after the program. MegaMan, SearchMan, and the NetPolice re-delete the Darkloids while Dark ProtoMan goes straight for the program that Chaud and Anetta are working with. Meanwhile, Bass appears and revives ShadeMan.

With the help of Yai and his friends, Lan blasts off to space to stop Dr. Regal against the NetSavers' orders. JunkDataMan also reappears to help the kids by giving MegaMan JunkDataSoul to clear the space of junk. When Lan reaches the station, he's instead confronted by Dark ProtoMan, and after the battle, the space station sends on a crash-course to Earth. However, JunkDataMan is able to rescue the children at the last moment.

When Ms. Mari witnesses the apparent death of Ms. Yuri, she reveals the truth about her twin sister that she was separated from at a young age. However, Ms. Yuri returns to life and is ordered to kill her sister. She takes Misaki hostage and reveals that she's a superhuman descendant of Duo, an intergalactic force that will soon arrive on Earth. Lan and the kids intervene and try to stop Ms. Yuri who uses a Dark SynchroChip to fight, but she is swayed against Nebula. In the end, Dark ProtoMan appears and strikes, presumably killing both Ms. Yuri and Misaki.

The NetSavers and Lan's friends have devised a plan to bring ProtoMan back from the darkness with a VaccineChip. Luring him into a trap at a deserted hotel, the plan is put into motion, but the chip fails. Chaud performs CrossFusion with Dark ProtoMan to try and cure him, sending the two into a world of memories where they battle with the darkness. The darkness is eventually alleviated, but Chaud and ProtoMan are both hospitalized after the battle.

Revived, ShadeMan plans to get revenge on Dr. Regal. First, he captures Rush and uses his technology to appear in the real world without the aid of a Dimensional Area. He goes on a rampage through DenTech City to find Dr. Regal, but Lan intervenes. However, once Dr. Regal appears, he unveils a tower of Dimensional Area Converters and covers the entire planet.

Dr. Regal uses a Dark SynchroChip to fuse with his NetNavi, LaserMan, and then proceeds to rip ShadeMan to shreds. Then, giant-sized LaserMen begin attacking cities throughout the world. Lan uses DoubleSoul during CrossFusion to fight Regal, but it zaps his power. CrossFusion ProtoMan reappears to help fight, but Regal proceeds to attack the Sci-Labs. However, the pleas of the NetNavis' souls (powering the Dimensional Area Converters) revives Lan and he achieves FullSynchro, completely destroying Dr. Regal. With peace restored, everyone watches a night sky of shooting stars, including Ms. Yuri who claims "As one chapter ends, another one begins."

The NetSavers are in investigation with the Sci-Lab over the strange comet that has appeared in Earth's atmosphere. Soon, strange activity begins occurring when giant-sized Mettaur viruses begin terrorizing DenTech City. Lan and Chaud manage to defeat them, but MegaMan finds himself captured by none-other-than Bass. He tells MegaMan that he is after his "Ultimate Program" so he can fight off Duo. As Lan and Chaud rush to his rescue, they encounter an old rival, Dr. Wily, who seems to know what's going on.

ProtoMan arrives to help ward off Bass, but more giant-sized viruses continue appearing in the real world. Lan and Chaud prepare to send their NetNavis to the comet, but Bass intervenes in hopes of overcoming the power that threatens Earth himself. Bass meets Slur who swiftly defeats him. Slur is a subordinate of Duo, an intergalactic force threatening to erase Earth after Dr. Regal's activity with darkness. However, Lan and Chaud convince him to spare their planet, and Duo challenges them to prove humankind's worth. After the incident, Lan receives a marking on the palm of his hand, the Crest of Duo.

BlazeQuest releases new PET models called Progress PETs. Meanwhile, while shooting a commercial for BlazeQuest, Lan meets Inukai, a zookeeper who is abusive to the animals. When Inukai gets in trouble, his frustration attracts Slur, and he is given Asteroid SavageMan to get revenge. Asteroid NetNavis are able to appear in the real world without Dimensional Areas, causing problems with Lan and Chaud, but Dr. Wily helps in the production of a Dimensional Area Generator, allowing the Sci-Labs to create them on command.

Mameo, a boy attending Lan's school, hates vegetables. Slur targets him and gives him Asteroid VineMan who can help destroy all of the vegetables in the world. This enrages Lan since vegetables are a prominent ingredient in curry, so Lan and Chaud track Mameo down. However, VineMan turns on Mameo, so Lan and Chaud must rescue him from his own NetNavi.

While investigating a NetSaver case, Lan notices helicopter pilot Charlie Airstar at the scene of the crimes. Lan presumes Charlie is the culprit, but Charlie is really tracking the true criminal on his own: director of DNN network, Sunayama (and even has the nerve of pursuing Sunayama to Lan's school). Sunayama uses Asteroid DesertMan to fight back, but MegaMan and ProtoMan team up with Charlie's GyroMan to stop him.

Clumsy Yui receives Asteroid StoneMan who gives her the power to turn anything she touches into stone. Panicking, Yui soon transforms the entire business complex and everyone inside into statues. Lan, who is returning an item Yui lost, encounters the problem and battles with StoneMan through Cross Fusion, as Yui had panicked and slotted the Dimensional Chip in.

Lan and Chaud represent BlazeQuest in a car race where NetNavis operate racecars in the real world and get into some comical arguments in the progress. Another participant, Rei Saiko, has mysteriously moved up in the tournament thanks to Rei's new NetNavi, Asteroid FlashMan, who has been cheating in the races. MegaMan and ProtoMan catch FlashMan in the act and are forced to battle with him by Cross Fusing, but Rei escapes before he can be arrested.

Lan and Chaud are led to Netopia to investigate a strange virus disturbance near a research center. There, strange holographic visions of the past appear, and viruses previously believed to be extinct attack in the real world. MegaMan and ProtoMan are also attacked, but they're rescued by a NetNavi named Colonel. After the incident, Chaud receives the Crest of Duo, and he decides to continue investigation in Netopia while Lan returns home.

Mr. Gauss's daughter Tesla announces the formation of a new net-crime syndicate called Neo WWW, and their first mission is to rescue the imprisoned Mr. Gauss. Lan and the NetSavers attempt to intervene, but with the aid of Inukai, Rei, and Sunayama who have all joined Tesla, Mr. Gauss is rescued and Tesla becomes the new operator of MagnetMan.

When film writer Viddy Narcy becomes enraged over the criticism of his latest work, Slur gives him Asteroid VideoMan. With VideoMan's help, Viddy begins painting the city in pink, including part of Lan's face. Lan teams up with Charlie to track Viddy down, and by forming GyroSoul with GyroMan, VideoMan is defeated. But as Viddy escapes, he encounters Sunayama who offers him a position in Neo WWW.

Inukai begins an attack by transforming automobiles throughout DenTech City into wild animals. Lan and Famous investigate the situation and MegaMan goes to battle with SavageMan but encounters all four Neo WWW NetNavis at once. Colonel reappears and rescues MegaMan in the end.

While visiting Dex in Jawaii, Lan meets Dingo, a fellow lover of curry. The two become quick rivals and Lan challenges him to a NetBattle with TomahawkMan. Meanwhile, Viddy plans to bury the entire island in a giant wave of curry sauce, so Lan and Dingo infiltrate his giant fish airship to stop him with some help from Dex, who Viddy kidnapped to make the curry sauce.

Lan meets a girl named Jasmine from the country of Choina. To complete her training as a pharmacist, Jasmine seeks a rare flower, and Lan agrees to help her. However, a man named Bengel in a medicine company hopes to steal the medicine that Jasmine is concocting, so he kidnaps Jasmine and threatens to delete her NetNavi Meddy if she doesn't give up her secrets. Lan and MegaMan manage to rescue the two from the perilous situation.

BubbleMan returns, and this time, he seeks a rare treasure hidden in the depths of the internet. He joins up with IceMan and SpoutMan to undergo this mission, but MegaMan and Roll are close behind to keep the young NetNavis out of trouble. MagnetMan also tails the group, hoping to snag the treasure for himself.

Chaud teams up with Raoul and ThunderMan to investigate missing NetNavis in Netopia. They track the crime down to Ivan Chilliski who was given Asteroid FridgeMan to undergo such crimes. Chaud and Raoul dupe him into revealing himself by posing as the afro-wig villains from Axess, and Chaud uses CrossFusion to battle with FridgeMan.

Mac and Harry, two criminals Manuela is pursuing, receive Asteroid GravityMan, and to get revenge on Manuela, they use him to shift gravity and make Manuela believe she is putting on weight. As a result, Manuela is overcome with the need to diet and exercise. However, Mac and Harry unintentionally appear in a submarine with the NetSavers during a virus examination, and they lose control of their NetNavi. Raika rejoins the cast at the end.

DarkChips have begun spreading through DenTech City again, so Lan begins an investigation in a factory to catch the culprits distributing the chips. He encounters Inukai and Rei who overcome him in battle. However, Raika reappears, now using CrossFusion to overcome the Neo WWW members.

Lan and Raika investigate the disappearance of ancient weapons being stolen from museums, and Raika suspects that his old friend Iriya may be operating Asteroid JapanMan who is responsible for the crimes. However, Iriya may be innocent when he tries to protect Raika from JapanMan. Lan and Raika delete JapanMan and bring Iriya back to his senses. Before returning home to Sharo, Raika receives the Crest of Duo.

Asteroid MoltanicMan was given to a criminal, but after an incident, a war-torn MoltanicMan drifts through the internet and finds himself in the PET of young fireworks-maker Fyrefox. Fyrefox is delighted to have a NetNavi after the loss of his own, and Fyrefox's friendship gradually sways MoltanicMan away from evil. However, MoltanicMan's original NetOp reappears, unwilling to give up his partner in crime to Fyrefox.

Lan and Dr. Hikari visit Taneka Island to help with the launch of a satellite. Meanwhile, Tesla is also visiting the island, planning to hijack the satellite. Before her attack, she encounters Charlie who quickly falls for her, and the two develop a flirtatious relationship. However, when Charlie discovers that the girl is really Tesla of Neo WWW, he rushes to the satellite to stop her attack.

Misaki finally awakens after the coma Dark ProtoMan put him into at Axess's conclusion, but he's discerned to learn that Ms. Yuri was never found. Meanwhile, Colonel faces Slur but is horribly damaged, so he's taken in to the Sci-Labs to recover. Before he can be questioned, he vanishes again. Back at the hospital, Asteroid BlasterMan attacks, and Misaki uses PrismMan to confront him. When cornered, Misaki is rescued than none-other-than Ms. Yuri who uses CrossFusion to defeat BlasterMan.

Ms. Mari's class is going on a field trip to the WaterWorks-main control center for all of the water systems in DenTech City. But there's a problem with the pipes! The nerdiest villain on the Net, BubbleMan, has an evil plan to turn every fixture in the city into a flooding fountain. A Dimensional Area forms around the WaterWorks and BubbleMan materializes to take control of the system. Lan and MegaMan CrossFuse to battle the bubbly bandito, but the power of the Fusion soon fails. Our heroes seem to have a problem communicating--and unless Lan and MegaMan can work together as a team, DenTech City is sunk!!

The Darkloids are at it again! When electrical energy begins to surge all over the city, NetSaver Lan and MegaMan are called in to investigate. They find FlashMan on a dastardly dark mission of blindingly bright madness! His plan? To overload, then drain every circuit in the system! After defeating MegaMan in battle, FlashMan is rewarded with a powerful ""DarkChip"" from ShadeMan and ups the wattage on his rampage. Roll shows up and distracts FlashMan to give MegaMan time to recover, but is quickly overpowered. Just as FlashMan is about to delete MegaMan and Roll, the two unlock a brand new power called ""DoubleSoul,"" and pull the plug on the degenerate Darkloid!

Ms. Mari takes Lan and some of the other kids on a field trip to the ancient Yokayoka Hot Springs, but Lan finds more fun NetBattling a local employee named Tamako. That is, until he discovers Tamako and her NetNavi HeavyMetalMan are so obsessed with NetBattling they won't let Lan do anything else. Even worse, the goofiest villain on the Net, BubbleMan, has returned to get his revenge on MegaMan and Lan, even if it takes opening a Dimensional Area to do it!

Dex has returned to DenTech City and, giving up his dreams of being the strongest NetBattler, has now embraced a life as a curry chef. Dingo also moves to DenTech to work for the original WWW's curry shop. Meanwhile, Sunayama and DesertMan work together in their latest scheme, but Yahoot, Dex, and Dingo work together to stop him.

A bowling craze is sweeping NetCity, and when Higsby wins bowling tickets, he sees a perfect opportunity to finally take Ms. Mari out on a date. Of course, he needs lots of help from Lan and Maylu just to get the date, and then, worried about embarrassing himself while bowling, he schemes with NumberMan to cheat! But that's far from the worst of it. Infected by a DarkChip, BowlMan starts wrecking the Human World and then even comes to the Human World! Lan and MegaMan CrossFuse and take care of him, but it looks like Higsby's cheating stunt has left him on the outs with Ms. Mari. That is, until she reveals that she'll go on another date with him.

Mr. Match is back in town--but that's the least of Lan's problems! The CyberWorld is being attacked by a flowery fiend with a desire to drain all the Data in DenTech City, and then the world! As computers, traffic systems and just about everything else electronic shuts down, Agent Lan and MegaMan are called into action to figure out how to stop the botanical nightmare, but soon MegaMan becomes trapped by the viney villain VineMan. On a mission of his own, HeatMan suddenly appears and frees MegaMan, but is badly damaged in the battle. As Famous helps Mr. Match recover HeatMan's data, somehow TorchMan's spirit is revived in the process! As MegaMan enters the final showdown with VineMan, he's soon joined by TorchMan to go DoubleSoul and fry the vicious vegetable!!

Lan scores free passes for himself and his friends to check out the new Science and Technology Center before it's Grand Opening. But really, he's been sent there on a secret mission by Mr. Famous to check out a potential virus infection. Little does Lan realize that the virus is a plant by SavageMan and ShadeMan to trap MegaMan in order to exact their revenge, but he sure finds out fast enough. He also learns that, with the DarkChip sent by the Mysterious Man, that revenge expands into the Human World, where viruses and SavageMan himself come after Lan and his friends!

Dex finally returns home from Jawaii Island, where for months he's been in training with the ex-World Three gang to become the ultimate NetBattler. Meanwhile, things are heating up in DenTech City as BurnerMan unleashes a hot blast of chaos throughout the town. The Darkloid has crippled the natural gas system as part of ShadeMan's nasty plan for domination. Lan and MegaMan spring into action, but they're interrupted by Dex and GutsMan--on a mission of their own to try out their new so-called skills. Dex joins forces with Lan to stop BurnerMan's rampage, but only because he wants to defeat Lan himself! Have the old friends become new enemies--or is Dex just dazed and confused?

Lan and Dex travel to Choina in hopes of finding a medicine for an ill panda bear in DenTech's zoo. There, they meet Cardamom, the grandfather of Jasmine. Meanwhile, many people in Choina wish to steal Cardamom's medicinal secrets, so Lan and Dex team up with Jasmine to help stop such a villain.

Someone is illegally giving out DarkChips, the powerful BattleChips that increase a NetNavi's strength but destroy its connection with its NetOp and turn the Navi into a Darkloid. Mr. Famous puts Lan and MegaMan on the trail of the mysterious chips. As the investigation unfolds, Lan and MegaMan have to battle NetNavi SpikeMan, and they also cross paths with a woman who looks just like Ms. Mari--and might be her evil twin sister!

ShadeMan and the Mysterious Man need rare metal to create DarkChips as part of their evil plan to take over the world. But the valuable metal is locked away in a high security building, so they create a Dimensional Area and send in the bumbling BubbleMan to steal it from the safe. When he fails, BurnerMan takes on the task. He completes the mission, delivers the goods to his bosses and prepares for another heist. Meanwhile, Lan and MegaMan spring into action to stop the villains, only to discover that the only way into the Dimensional Area is by CrossFusing at exactly the right moment. But can they perfect the process before all the precious rare metal is pilfered?

Lan can't believe that his dad would give a SynchroChip to Chaud, but that's exactly what Dr. Hikari did. And even worse, he reveals that Chaud and ProtoMan had a stronger CrossFusion than Lan and MegaMan! Lan has to run off on an errand for Maylu, but it turns out that the errand was just a trick by Yai to get Lan, Maylu, Ms. Mari, and Rush into an elevator that turns into a robot and flies them to KingLand. The data from Ayano Tech's latest video-game has been stolen, and it's up to Lan and his friends to get it back!

Yai holds a NetNavi design contest, and Viddy is so thrilled to participate that he quits his job with Neo WWW. However, upon winning the contest, Viddy is disqualified because the contest is restricted to children. Enraged, Viddy begins transforming AyanoTech's game characters into rabbits, but Lan and MegaMan intervene to stop Viddy's rampage. Viddy returns to his life at Neo WWW.

It's Tesla's birthday, and she desires more than anything her own SynchroChip. Through a series of crimes, the Neo WWW is able to retrieve her one, and she uses it to overcome Lan in battle. In the end, he is rescued by Ms. Yuri, but not before she has a special reunion with her twin sister Ms. Mari.

Sharo and Brightland cooperate in the production of a CrossFusion Research Institute, but Asteroid AirMan is sent to destroy it. Raika and Princess Pride work together to stop him, and they're chased to an abandoned castle amidst an ice storm where more secrets to this attack are unveiled. Raika ultimately defeats AirMan, and Pride receives her own Crest of Duo.

Lan meets Route, a guide program at an automobiles museum. Meanwhile, criminal Ken has to steal cars in order to rescue his girlfriend from a mob leader, and he is given Asteroid BrightMan to do so. Lan intervenes but is overpowered by BrightMan, so Route sacrifices herself in order to help defeat the Asteroid. However, Route is revived from back-up data, and peace is temporarily restored.

The Air Show Festival has arrived! Lan and MegaMan would like to enjoy it, but a Cyber World villain-for-hire named ShadowMan has been brought in by the Mysterious Man to destroy the Control X traffic management systems around the world, and that includes the new one controlling the Air Show. When MegaMan swings into action, he discovers a hard-hearted fellow NetNavi called SearchMan who is also after ShadowMan. And SearchMan is perfectly willing to delete anything in his way--even MegaMan.

Lan becomes tired from constantly battling the Neo WWW, so Dex decides he wants to perform CrossFusion and help in the battle. He confronts Famous who uses Rush to create the Rush SynchroChip to help make it possible. Dex and Maylu accompany Lan to a dinosaur theme park where Viddy strikes, but Lan is too tired to battle. Dex attempts CrossFusion and fails, so in order to save the day, Maylu tries it. Surprisingly, she CrossFuses flawlessly and helps Lan defeat Viddy.

Lan finds a warehouse full of DarkChips, and he starts to think he's the best NetSaver on Earth. He's sure that it'll be easy for him to find the factory that's making the DarkChips. Meanwhile, Chaud has plans of his own to find the factory: he follows Ms. Yuri. At the warehouse, Lan stumbles upon the factory and also upon DesertMan, who's so powerful that Lan and MegaMan can't defeat him. Just when it seems that it's curtains for them, CrossFusion ProtoMan shows up and helps to save the day.

An investigation by Chaud in Netopia against a man named Rat leads to some shocking discoveries. A man named Jackass used the same crime tactics that Rat did, but his attacks were decades in the past, and Colonel was responsible for stopping him. Considering Colonel still exists in the present time, Chaud contemplates the true nature of his character. Chaud and Raoul ultimately capture Rat and defeat his Asteroid DrillMan, but not before his plan was put into motion, causing locks all over the world to suddenly unlock.

When Dex does a delivery for Yahoot's curry shop on Jawaii Island, the customer cons him into trading the food for a mysterious box. Yahoot scolds him for not collecting the cash, but soon finds out the seemingly worthless box is actually a powerful NetWrecker machine, capable of altering a NetNavi's data and increasing its power and size to unbeatable proportions! When Lan and the gang land on the island for a visit, he and MegaMan soon find themselves in a NetBattle against Dex and his amazing machine! In his efforts to finally defeat Lan, Dex boosts up GutsMan's power, but he loses control of the big metal ape, sending GutsMan stomping through the streets with Roll as his prisoner. This ""Incredible Guts"" seems unstoppable, and worse yet, nobody knows how to change him back!!

When a newspaper prints Tesla's age as thirty, she becomes enraged. During a robot battle convention, she hijacks a robot named Thirty and attacks the NetPolice. After a malfunction, the robot goes speeding after Lan and Fyrefox through DenTech City. Lan CrossFuses to battle with Tesla while Fyrefox sends MoltanicMan inside Thirty to prevent it from self-destructing.

Ms. Mari takes Lan and Maylu to an International Exhibition being held at the amazing new Sea Tower building that rises up from the middle of the harbor, but their visit is interruped when ever-ready Net rival Tamako appears and goads Lan into a NetBattle. But soon there's another interruption: SavageMan shows up, sent by the Mysterious Man to take care of MegaMan and Lan in exchange for the DarkChips he craves. The forces of evil aren't messing around this time: they've even sent in Ms. Yuri to destroy the Sea Tower with our heroes inside!

Through Chaud's research, he knows more information regarding Colonel and his NetOp Baryl.[1] Meanwhile, a shift in time and space revives ShadeMan moments before LaserMan deleted him in Axess. He fights with Lan and Chaud, and Ms. Yuri helps, revealing that she, too, has a Crest of Duo. ShadeMan reunites with BubbleMan and begins their latest scheme to travel twenty years into the past, before the network was created, and overrun the world with Darkloids. MegaMan attempts to stop him but fails, receiving a painful bite on the neck as he falls.

Lan shows up to save a stalled truck on the train tracks, but he finds that a stranger already took care of the situation. Later, Lan meets the stranger, Raika, a NetSaver from Sharo, and his NetNavi, SearchMan, who had helped MegaMan and Lan defeat ShadowMan earlier. Raika is unimpressed by Lan, feeling he relies too much on the SynchroChip and not enough on his intelligence. And when VideoMan attacks, it seems that Raika is right: CrossFusion MegaMan can't defeat VideoMan, but luckily Raika destroys the Dimensional Area generator and gets rid of VideoMan before he can delete CrossFusion MegaMan.

MegaMan dives into the space-time tunnel and follows ShadeMan twenty years into the past. There, he encounters Colonel and teams up with him to save the future. However, the bite left by ShadeMan on MegaMan's neck infuses him with evil energy, transforming his soul into darkness. Lan rushes to connect with MegaMan again, hoping to install a VaccineChip and recover him. He does so just as ShadeMan is deleted, and MegaMan manages to stop his plan, returning the present time back to normal. As MegaMan returns to his time, the dark energy separates from his body and vanishes.

Shanka, a girl from Dingo's tribe, requests to return a stolen totem pole back to her village when it's discovered in a museum. However, Viddy and Inukai steal the totem pole along with other rare items, so Lan, Dingo, and Shanka work together to recover the ancient relics. In the end, Dingo receives the Crest of Duo.

After using the DarkChips too many times, the Darkloids begin to depend on them just to function, so DesertMan breaks into NetPolice headquarters to steal some confiscated DarkChips. Lan and MegaMan rush into action and manage to stop the sandy scoundrel and capture him. Dr. Hikari examines DesertMan and tells the others that he thinks Darkloids might actually be a new digital creation that evolved on its own--unlike every other Navi, which were at least partly created by humans. ShadeMan learns of DesertMan's capture and sends FlashMan to free him, but ShadeMan realizes that FlashMan might need a little help. With the Mysterious Man's assistance, ShadeMan captures Keifer and Manuela and offers to return them in exchange for DesertMan's release.

Jasmine returns to DenTech City to take care of an injured dolphin named Hoshi (meaning "star"). Hoshi was injured when being used by the Neo WWW to smuggle DarkChips. Lan, Yahoot, Dex, and Jasmine team up to defeat Inukai and SavageMan in their latest schemes. In the end, Jasmine receives the Crest of Duo.

At a convention center, a Ms. Tiara contest is held with a chance for girls to win a golden tiara, and many girls from DenTech City enter. A rivalry quickly builds between Maddy and Tesla. Tesla attempts to steal the tiara, so Charlie appears to intervene, and all of the girls aid Lan in Neo WWW's defeat. Ms. Mari ultimately wins the contest, and both Charlie and Tesla receive Crests of Duo.

Higsby has put together his very own NetBattle tournament, but it looks like it's going to be a disaster. Only Lan and his friends have entered. Even worse, Shuko, who has a reputation as being so unlucky that she ruins everything around her, wants to enter. Shuko's bad luck starts to affect the others, and she actually wins! But when she goes to cook up the rice she won as the tournament's first prize, she learns that Higsby's power is out. She's sure that she caused the problems, and she's very upset. Looking to cheer her up, her NetNavi SpoutMan goes to the power plant to fix the problem. But when SpoutMan starts crying, cyber water gushes everywhere and threatens to destroy not only the power plant, but also the entire CyberWorld!

MegaMan has startling dreams where he murders his NetNavi friends, and he becomes nervous when he learns his friends were injured the night before. Though MegaMan's system tests normal, MegaMan begins causing mischief, leading to his eventual arrest. After an emotional separation, Lan realizes that he isn't MegaMan, and the NetNavi unveils himself as Dark MegaMan. The real MegaMan has been captured by Darkloids CosmoMan, LarkMan, BlizzardMan, and CloudMan. Ms. Yuri helps Lan rescue his NetNavi, and ShadowMan even reappears to assist. The Darkloids thus escape.

Having gotten a hold of the Darkloids' Dimensional Area generator, SciLab has brought in Dr. Regal to investigate its mysterious energy source. Dr. Regal finds a way to power up the generator, but then a Darkloid named SparkMan shows up and uses the energy of the generator to drain the strength from CrossFusion MegaMan and CrossFusion ProtoMan during a battle! SparkMan succeeds with his mission to destroy the generator, and the secret of its power source comes out--it runs on data from captured NetNavis.

BubbleMan becomes a pawn in the power struggle between ShadeMan and the Mysterious Man. Meanwhile, the Mysterious Man sends BurnerMan on a mission to cause a devastating volcanic eruption. The site happens to be right under the hot springs Lan and the gang have gone to for vacation. As the tiny town begins heating up and melting down, Chaud joins Lan to stop BurnerMan from superheating the magma deep below the earth and causing massive molten mayhem. But can the NetSavers stop their fiery foe in time?

Dr. Hikari researches the Crests of Duo and discovers that those marked with it have higher synchro-ratings, meaning CrossFusion is more possible with them. Meanwhile, Yai is planning a fireworks party, so she urges Lan to bring Fyrefox and Mr. Match to help with the festivities. However, BlizzardMan and CloudMan attack with orders to delete MegaMan, and they transform the hall into a raging blizzard. Lan, Dex, Mr. Match, Dingo, and Fyrefox all team up to overcome the Darkloids, and Fyrefox is able to delete BlizzardMan in the real world using a firework dispenser. Fyrefox thus receives the Crest of Duo.

VideoMan tricks MegaMan into coming to a video store and then records his movements and copies his image. VideoMan then transfers MegaMan's likeness to videotapes around the world so that every time someone watches one, the MegaMan copy appears and causes trouble. Lan and Chaud finally figure out how to erase the tapes using a magnetic field, and as CrossFusion MegaMan and CrossFusion ProtoMan, they erase all the MegaMan copies and delete VideoMan as well.

Lan introduces Maylu to Jasmine, but she quickly becomes jealous of the relationship the two have developed. Having been marked by Duo, Lan and Jasmine can see Duo's comet, but Maylu cannot. Likewise, Meddy and Roll compete for MegaMan's affection. Meanwhile, a fortune-teller named Romeda wants to make a huge prediction, so her NetNavi Asteroid NovaMan causes a meteor to come crashing down towards Earth. Maylu intervenes and helps Lan defeat NovaMan and stop the meteor. Together, they stand and watch Duo's comet, signifying Maylu too received the Crest of Duo.

A girl named Anetta lost her NetNavi in the past, and she's lead to believe that Chaud's ProtoMan was the one who deleted her. She works with Ms. Yuri and the Darkloids to try and infect ProtoMan with a DarkChip, but will she succeed?

Neo WWW calculate a plan to prevent the creation of Dimensional Areas. SavageMan destroys the Sci-Labs's Dimensional Generator, but the attack deletes SavageMan and hospitalizes Famous. Then, because of a solar eclipse, receiving Dimensional Area signals from across seas is impossible, and Neo WWW begins their attack with Lan unable to CrossFuse. The original WWW teams up with their old leader, Dr. Wily, to devise a plan against the Neo WWW. They prove victorious, and VideoMan is also deleted.

Lan and Chaud travel to Nebula's base where Anetta is being held hostage. Once there, however, ShadeMan materializes in the real world and they battle with him using Cross Fusion. The ship in which the base is being held on is going to explode, so Lan and Chaud need to evacuate... but in the cyber world, ShadeMan is fighting with MegaMan and ProtoMan. Chaud is tempted with a DarkChip to rescue ProtoMan from deletion, but will he use it?

Lan and Maylu visit an orbital elevator that reaches into space. Once there, however, they become entangled in Tesla's next plan as she hijacks the elevator. Lan and Maylu use CrossFusion to battle DesertMan and FlashMan, succeeding in the deletion of both. As the final Neo WWW members are arrested, Tesla suddenly vanishes, and her four subordinates' memories are erased. Dark MegaMan has taken Tesla hostage in her own hideout.

MegaMan tries to offer comfort to Chaud, who has just lost his NetNavi ProtoMan. Meanwhile, Lan is asked to stand guard at a fashion show that shows off special new holographic technology. Maylu is also there, but things turn for the worse when Yuri tries to steal the technology. SparkMan appears to help her with her mission, but Chaud also arrives to stop Yuri himself.

Dark MegaMan's Darkloids invade NetCity and then retaliate against Lan in the real world, destroying his SynchroChip. To have it repaired, Lan travels to Sharo's CrossFusion Research Institute where Dr. Hikari is stationed. Along the way, the Darkloids attack again, but Lan is rescued by Raika and Charlie, and he is surprised to discover that Charlie has now CrossFused as well.

The Darkloids take over a large excavation machine and begin rampaging through Sharo. In order to stop them, the CrossFusion Members join together, including Raika, Charlie, Dingo, Jasmine, Princess Pride, and Fyrefox. While they battle, Lan's SynchroChip is stolen by Dusk, ShadowMan's NetOp. Ms. Yuri and SpikeMan intervene and Lan recovers the chip, but as Dusk escapes, he receives the Crest of Duo. The Darkloids escape, and it's revealed that Dr. Regal is commanding the Darkloids.

Dusk is an assassin commanded to delete MegaMan, but he hesitates for the Crest of Duo marks him as Lan's ally. Meanwhile, a bank robber similar to Dusk named Kawase uses Asteroid SwordMan in his crimes, so Lan and Dingo intervene. Dr. Wily offers Dusk the opportunity to live his own life outside of hired assassin work by giving him a SynchroChip, and with it, Dusk CrossFuses and rescues the boys.

Dr. Hikari and Famous bring the CrossFusion Members together at the beach for special training, but the training session is really just a relaxing vacation in the sun to help calm their nerves. Yai and Anetta also attend, as well as the original WWW members. The gang ends up exploring a haunted house, and Maylu continues to fight Jasmine for Lan's affection.

The CrossFusion Members meet with Chaud to explore ancient ruins discovered in Netopia which bare Duo's symbol. Inside, a holographic image tells of an alien race that travels to planets via Duo's comet and destroys civilizations that are deemed dangerous. Slur becomes enraged that the heroes have discovered the past of her race and commands the destruction of the ruins. The children barely manage to escape in time.

The CrossFusion Members formulate a plan to infiltrate Neo WWW's hideout and rescue Tesla. Also, the member's Crests of Duo have mysteriously faded away, the first three victims being Chaud, Raika, and Princes Pride. Count Zap also assists Mr. Gauss in the rescue of his niece. To pass security, the members must scan their hands. But once inside, the Darkloids Cloudman and LarkMan attack. Battling up to the top, they reach Dark MegaMan, who reveals that Mr. Gauss tricked the members into the tower in exchange for Tesla. The hand scans gave Dark MegaMan the data that rested within Duo's Crests. As the members escape the tower, Tesla CrossFuses and vanishes.

Charlie is startled to discover Tesla has been sleeping in his apartment. Meanwhile, Dark MegaMan lures Ms. Yuri into a trap to steal her Crest of Duo. When she refuses to comply, Dr. Regal then appears and steals it himself. Lan, Charlie, and Tesla battle with the remaining Darkloids, deleting CosmoMan and forcing Dark MegaMan to retreat. Dr. Wily explains that Dr. Regal needs the data within the Crests of Duo to achieve access to the power within Duo's comet. Dr. Regal has planned such a thing for decades as he had already taken Baryl's Crest twenty years ago when Baryl was alive.

The Asteroids begin invading Earth, and the CrossFusion Members fight to ward them off. However, until Slur is defeated, the numbers will only grow, so while the members battle the Asteroid invasion, MegaMan, ProtoMan, SearchMan, and Colonel jack-in to take Slur down themselves. However, their efforts are futile, and Slur easily overcomes them on her own.

Thirty years ago, Duo's comet had crashed on Earth, and Dr. Regal plans to travel through space and time to absorb its power. MegaMan, ProtoMan, SearchMan, and Colonel rush through time to thwart Dark MegaMan who was sent to help Dr. Regal gain access to the comet. However, Dark MegaMan plans to absorb the power himself and become the ultimate NetNavi, but Slur refuses to allow him to do so by deleting him. Before fading away, Dark MegaMan self-destructs and prevents Dr. Regal from succeeding. The heroes return home, and the renmants of Dark MegaMan's being rejoin with MegaMan's soul, and MegaMan forgives him.

Duo begins to erase the Earth, and in order to stop him, all thirteen CrossFusion Members must join together. However, Baryl has already died. Dr. Wily of the past works with Dr. Wily of the future to send Baryl through time and space using the Spectrum program. Once Baryl arrives in Lan's time, he receives a SynchroChip and uses CrossFusion to help his allies take down another invasion of Asteroids.

Bass reappears and now infused with the power of Nebula Grey, he deletes Slur. Meanwhile, Dr. Regal gains access to Duo's power and begins his attack on Earth, but Duo kills him before beginning the erasure of Earth. The CrossFusion Members travel to Duo's comet, avoiding demise as the Earth vanishes. They confront Duo, begging him to reverse the erasure, but Duo cannot comprehend their pleas, having more interest in CrossFusion instead, a technology similar to his own race's.

BubbleMan, who was frozen in cyber space by Colonel, finds himself freed when a strange energy appears before him. Left behind is an infant NetNavi. He carries it to NetCity before collapsing and being found by Roll and the others. Meanwhile, strange disturbances appear in the real world as two gigantic cloaked beasts begin battling. Lan, Chaud, and Raika intervene, and the beasts move their battle to the internet. When MegaMan battles with them, the infant's power combines with his own, and MegaMan defeats the beasts using two new styles modeled after the beasts.

Two NetNavis known as Zoanoroids are at war on the internet, one praising the lion Gregar (Zoano VineMan) and the other worshipping falcon Falzar (Zoano SparkMan). The Zoanoroids claim to descend from a world called "Beyondard." As they battle, MegaMan and ProtoMan intervene. Meanwhile, Roll takes care of the infant NetNavi who MegaMan decides to name "Trill."

Famous assists Makoto in the production of CopyBots (known as "Copyroids" in Japanese), robots that allow NetNavis to interact in the real world. However, once completed, Zoano Punk appears and forces Makoto to build more CopyBots for his army. Lan and Chaud learn of this and assist Famous in Makoto's rescue, but not before a truck-load of CopyBots are delivered to the Falzar army. Meanwhile Trill "grows" and acquires the ability to speak after a long sleep.

The NetSavers receive word of a phantom battleship, so Lan investigates. The ship is being controlled by Zoano FlameMan who plans to use it to destroy a warehouse on an island where Falzar's CopyBots are being held. MegaMan battles with FlameMan, but Trill, who is insistent on showing MegaMan that he is not afraid of ghosts, gets in the way.

Yai has moved back to DenTech City, and as a treat to her friends, she takes them to a holographic animal exhibit that's still under construction. However, the exhibit malfunctions and the children are chased by deformed zoo animals. The NetNavis are jacked in to stop the mess, but a crack in space is revealed, bringing prehistoric beast viruses from the world of Beyondard to threaten the heroes.

Chaud travels to Netopia to explore a military factory where BubbleMan was imprisoned by Colonel. There, he meets a mysterious young girl. Meanwhile, Zoano PharaohMan is capturing NetNavis and transforming them into followers of Gregar, including Zoano SparkMan. MegaMan intervenes and transforms with Trill into the Gregar Style to defeat the Zoanoroids, but as a result, loses control of his body and escapes into NetCity.

Lan's friends work together to try and subdue Gregar MegaMan who is rampaging through NetCity. Meanwhile, the mysterious girl appears before Lan asking of Trill before vanishing again. Later, a strange light forms over MegaMan, separating him from Trill before Trill also vanishes. A strange NetNavi attempts to return Trill to Beyondard, but he refuses, and ProtoMan appears to rescue the two from Zoano PharaohMan. ProtoMan takes Trill back to MegaMan.

The mysterious girl becomes a student in Lan's class, her name being Iris. Meanwhile, Zoano NumberMan appears and poses as Higsby's NumberMan in order to join his friends in visiting MegaMan (who is still recovering from last episode's damages). When the real NumberMan arrives, the two begin to battle until the true NumberMan is revealed, and the impostor escapes.

While playing in NetCity, IceMan encounters a fallen Zoanoroid FreezeMan, injured from a battle against Zoano StoneMan. FreezeMan was attempting to build a communication device for Falzar, and IceMan agrees to help retrieve it. When he returns, he finds FreezeMan in battle with StoneMan and attempts to protect his new friend, but FreezeMan sacrifices his own life to protect IceMan's. Both Zoanoroids fall, and IceMan builds a memorial grave for his deceased friend.

Lan and Maylu visit Dr. Hikari who is performing a deep-sea investigation. Zoano GateMan of Falzar and Zoano QuickMan of Gregar appear, both seeking to capture Trill. QuickMan battles with MegaMan while GateMan traps Dr. Hikari and Maylu underwater, threatening their lives if Trill isn't given up. QuickMan is defeated, but GateMan captures Trill and Lan's friends are not spared. MegaMan and Trill merge once more, and Beast-MegaMan assaults GateMan.

Zoano LarkMan is sent to help GateMan, and he turns his attention to Iris who has appeared on the ship with Lan. Meanwhile, Beast-MegaMan continues battling GateMan until the Zoanoroid is eventually deleted. As LarkMan prepares to defeat Lan and Iris, Chaud arrives on the scene and battles with the Zoanoroid using CrossFusion. Thus, everyone is saved, and Dr. Hikari and Maylu are returned from the depths of the ocean.

The NetSavers decide to capture the mysterious female NetNavi for information, and Trill is used as bait, but Zoano SnakeMan of Falzar and Zoano GutsMan of Gregar decide to try and capture Trill as well. MegaMan's friends battle with the Zoanoroids to protect Trill while Chaud tracks down Iris for answers. Iris and Trill descend from Beyondard, a world torn by the war between Gregar and Falzar, legendary cyber beasts. The key to restoring Beyondard lies within Trill, the "Synchronizer."

Zoano SnakeMan and Zoano GutsMan are subdued, but Zoano DarkMan is issued to capture Trill himself. The heroes are overwhelmed by his power, but Iris's NetNavi is able to assist in the protection of Trill, and she carefully houses him within Iris's PET. However, upon appearing in the real world with a CopyBot, DarkMan captures Iris and uses a device that opens a portal to Beyondard in the real world, and Lan, Chaud, Raika, Dingo, and Maylu are transported there with him.

Iris transports Trill away from her PET to somewhere in Beyondard where DarkMan cannot take him. Meanwhile, the children awaken in Beyondard, a world where both human and cyber worlds are one, and NetNavis and viruses can interact with humans directly. Maylu and Chaud reunite, as do Dingo and Raika, but Lan is left alone. He encounters Baryl and Colonel; they are Beyondard alternates of their original bodies and do not know Lan. When Zoano SnakeMan appears searching for Trill, MegaMan substantiates and defeats him.

Maylu and Chaud meet a train conductor named Al Ferry, operator of train-themed NetNavi ChargeMan. He lives in a village where the railroad network has prospered. However, Zoano JunkDataMan has been threatening the village by eating the tracks, and he sends viruses to cause more mischief. Chaud and Maylu offer to help, and ProtoMan substantiates to battle with JunkDataMan.

Lan travels to a fishing village where he meets a boy named Mick and rescues him from viruses. Mick takes Lan home to feast on a meal created by talented chef Pat Fahran. Pat has a dark past when a luxury liner she worked for was sunk by Zoano WhaleMan and she was the lone survivor. When Zoano WhaleMan appears to attack the village again, she seeks revenge with her NetNavi SlashMan. Lan also reunites with Trill.

Raika and Dingo meet an elderly man named Feng Tian who claims to know of Lan's location. However, his delinquent personality only causes trouble for the duo. Meanwhile, Beyondard alternates of Viddy and VideoMan harass the people of Amita, a village they have control over, so Raika and Dingo oppose them. Feng Tian also offers a hand with his own NetNavi, TenguMan. In the end, Raika and Dingo reunite with Lan.

While searching for Lan, Maylu and Chaud meet Moliarty and Press, NetOps of GroundMan and DustMan respectively. They're given a job by the Beyondard alternate of Ms. Millionaire to excavate through a rocky mountain for a precious item on the other side. Maylu and Chaud offer to help in the difficult excavation. (This is the only episode in the entire franchise where neither Lan nor MegaMan make an appearance.)

While searching for ingredients for Pat's curry, Dingo and Trill encounter DiveMan and follow him to a nearby lake castle. Inside, they discover that two humans, Captain Blackbeard and Yuika, are cooperating with Zoano DarkMan and have taken Iris prisoner. Dingo and Trill infiltrate the castle in hopes of rescuing Iris, but they must battle with Yuika's NetNavi, CircusMan. In the end, Iris is rescued.

Iris urges her friends to go to the Dimensional Area Laboratory, and they oblige. However, along the way, Zoano JapanMan appears and makes the journey difficult for the children, but their NetNavis substantiate and battle. Iris is damaged during battle, though, and revealed to be nothing more than a CopyBot. Reaching the lab, the children meet a holographic image of Tadashi, the Beyondard alternate of Lan's grandfather. He explains Beyondard's past before the children discover a war-torn Baryl outside of the lab.

An invasion is led by the Falzar army's Zoano CloudMan to destroy the Dimensional Area Laboratory. MegaMan, Roll, and TomahawkMan substantiate to fight back while Chaud and Raika operate the lab's defense system against the army. However, the great beast Falzar appears before the heroes, so MegaMan Beasts Out to retaliate. After the battle, the children are approached by an evil Colonel who threatens them, but Iris wards him off with her own energy.

On the way to the Wily Laboratory, Lan and his friends are attacked by Zoano CutMan, but a mysterious NetNavi EraseMan appears to delete CutMan himself. EraseMan is operated by the enigmatic boy named Dark Scythe who seems to have a connection to the Beyondard alternate of Maysa. Meanwhile, the younger brothers of CutMan formulate a plan to get revenge on Scythe by holding Maysa hostage.

Colonel has become a Zoanoroid and begins a rampage on the cities, and the children encounter him on their journey to the Wily Laboratory. Colonel attempts to capture Trill, but the children fight back. Meanwhile, Zoanoroids begin to invade DenTech City, and Dr. Hikari reassembles the CrossFusion Members to retaliate.

As Gregar and Falzar appear and begin battling, Blackbeard and Yuika (who are working for Beyondard Wily) succeed in capturing Trill. Falzar falls to Gregar, and Wily uses Trill as the synchronizer to combine both beasts into one. Creating the Super Cyber Beast Grezar and using it as his vessel, Wily begins to destroy both worlds.

The CrossFusion Members continue to deal with the Zoanoroid threat in DenTech City. Meanwhile, many Beyondard residents attempt to fight back against Wily but all fall short. In the end, in order to defeat Wily, Trill and MegaMan combine their powers and Lan performs Cross Fusion, merging into a new "Juuka Style." With this ultimate power, Lan is able to destroy Wily and close the portals between both worlds. With peace restored, Lan and his friends return home, but not before saying goodbye to new friends Trill and Iris.