Lan struggles with the memories of Beyondard, but everyone becomes well-adjusted to returning home. Peace isn't maintained for long, however, when strange cyber weeds appear all over a factory in Sharo, and Raika is forced to deal with substantiated viruses. The same thing soon occurs in DenTech City, and upon the defeat of the viruses, Lan faces a strange humanoid being with long blond hair.

As the NetSavers discuss the strange events, a man calling himself "Professor" announces his plans for world chaos before launching another attack with beastisized viruses. As Chaud uses CrossFusion to battle them, MegaMan jacks-in and encounters the humanoid being before known as Zero. MegaMan uses Beast Out to chase Zero away.

Lan and Chaud approach a power plant where more cyber plants and viruses have appeared, and they battle to delete them. However, Zero invades the Sci-Labs and escapes with a handful of valuable data. Lan learns from Yahoot that Professor was once a member of the WWW. Lan, Maylu, and Dex travel together to where Yahoot believes the Professor is hiding, but instead, they find a sushi factory.

While investigating the sushi factory, Lan and co. encounter many sushi chef robots, but the Professor uses them to try and ward off the intruders. However, they make their way to the depths of the sushi factory to discover that the Professor was indeed hiding down there and is planning to revive the Super Cyber Beast.

Professor sends a pack of viruses after Lan. Meanwhile, Chaud also appears in the factory to aid Lan, but Zero intervenes. Chaud battles with CrossFusion and fails, but Chaud's bond with his NetNavi sparks a change of heart in Zero. Refusing to be a pawn of Professor anymore, Zero departs to live his own life.

The Super Cyber Beast is revived prematurely, and in its incomplete form, it begins to rampage through NetCity. Professor escapes, so Lan and Chaud send MegaMan and ProtoMan into the internet to battle with the beast. Using Beast Out, MegaMan is able to destroy the new threat, temporarily ending Professor's reign of terror.

Blackbeard and Yuika cooperate with BubbleMan to steal materials for building giant-sized CopyBots. Both DiveMan and CircusMan jack-in to the giant CopyBot at once, creating a giant-sized combination of both NetNavis. Lan uses CrossFusion to thwart them.

Blackbeard and Yuika press Mr. Wily of DenTech City for cooperation, but Dusk arrives to chase them away. They learn that Mr. Wily is knowledgeable of CrossFusion and desire SynchroChips, and they devise a plan to steal some. However, they unintentionally steal Reverse SynchroChips, and upon using them, vanish into the cyber world.

Blackbeard and Yuika appear in the cyber world, CrossFused, and cause mischief while searching for Lan and MegaMan. However, if not stopped, their bodies would break down. Dusk enlists the help of Lan to stop them and reverse the effects of the SynchroChips.

Count Zap's wife, Ann, is feuding with her husband and desires the secrets of the Zap family estate, so she steals his PET, knowing that ElecMan is knowledgeable about the estate. Dex and Dingo challenge Ann to retrieve the PET, but she battles well with ElecMan, so Lan is called to help in the situation.

Count Zap and Ann fly to Kingland to investigate the family mansion for the treasure. Lan, Dex, Dingo, and Mr. Gauss tag along out of curiosity. The electric system of the mansion causes booby-traps, so everyone sends in their NetNavis to shut off the traps while they search for the treasure.

Moliarty and Press somehow become separated from Beyondard and appear in DenTech City, and they begin excavating holes throughout the city, unaware of the damage they're inflicting. Lan is sent to investigate the disturbance and believes them to be enemies, so MegaMan battles with GroundMan. However, Maylu, Chaud, and their respective Navis rush to the scene to clear their names.

A giant-sized Mettaur virus that was once a student of Moliarty and Press' has also appeared in DenTech City, and the infection of the Zero Virus has caused him to go berserk. Lan and Chaud CrossFuse to subdue him, but in the end, only a song sung by Moliarty and Press can calm the beast down.

When weather man Vic is fired for constantly making inaccurate forecasts, he stumbles upon BubbleMan who is now selling custom-built miniature-sized CopyBots. Vic decides to use one so that his NetNavi ElementMan can manipulate the weather, and he experiments at a public swimming pool that Lan is attending with his friends.

Throughout DenTech City, many criminals are being convicted before the NetSavers can investigate the scene of the crime. This is Prosecutor Ito who through a series of mishaps takes out his anger on the residents of DenTech City by convicting them unjustly. MegaMan and ProtoMan appear and battle with Ito's NetNavi, JudgeMan.

While NetNavis flee an incident in NetCity, GutsMan urges a cloaked figure to escape with him. The figure is actually Zero, and though he vanishes, the encounter with GutsMan touches his heart. Later, Zero attacks an energy center, and GutsMan is shocked to learn that his new friend is the culprit.

To get revenge on Zero for betraying him, Professor has built a Zero clone named Zero One to overwhelm the traitor. MegaMan helps Zero battle against his clone, but in the end, Zero sacrifices himself to destroy Zero One and help put Professor behind bars.

Maylu is excited about purchasing a trendy new handbag, and she drags Lan along for the ride. Meanwhile, one of BubbleMan's miniature CopyBots is unintentionally stolen, and he chases across DenTech City to retrieve one. When he mistakens the CopyBot for being inside Maylu's handbag, he steals it, forcing an enraged Maylu to chase after him.

Everyone becomes engrossed in a new Battle Station video game, but because Tory is busy with his violin/ice-skating lessons, he feels left out. However, Lan and Dex notice that IceMan is moving up in the ranks, and they suspect Tory is participating outside. However, they soon discover that this IceMan is a phantom duplicate.

A series of crimes are linked back to HatMan, the NetNavi of magician Mr. Hat. However, he has an alibi. Lan and Chaud meet Mr. Hat's son, Shuichi, who wants to be a great magician too. One day, however, HatMan hypnotizes Shuichi, and together, they cause problems. When MegaMan and ProtoMan confront him, the real HatMan appears, revealing that the HatMan controlling Shuichi was a phantom.

Raika and SearchMan assist in a virus protection program by acting as intruders to test the guard NetNavis, but the opponents that appear before SearchMan are MegaMan and ProtoMan. Raika suspects it's a prank, but MegaMan and ProtoMan then substantiate in the real world, and Raika is forced to use CrossFusion to battle them. In the end, the two are revealed to be phantoms.

Phantom NetNavis soon begin substantiating everywhere, and since no one can distinguish them from their original counterparts, NetNavis begin to distrust one another. Raika returns to DenTech City to tell of his encounter with Phantom MegaMan and ProtoMan, but something worse has happened. An unknown NetNavi has cut off access to the internet throughout the entire world.

NetNavis continue through uneasy times as they hide in NetCity, untrusting of one another. Lan, Chaud, and Raika send their NetNavis to the depths of the internet to battle with JammingMan, a NetNavi causing the disconnection from the internet. Upon his defeat, the three meet a strange NetNavi named Cache who begins to cackle while the world is blinded with a white light.

Lan begins a normal day of school and hanging with his friends, but something seems unusual. Soon, he realizes that no one in the world knows what a PET is. The world begins to fall apart, and his friends and family slowly transform into JammingMen. Recovering his PET, he brings himself back to reality where Cache has taken over the world and is transforming everything into cache data.

As Lan stands within the Sci-Labs, Cache appears and transforms him into cache data. Soon, MegaMan, ProtoMan, and SearchMan are also transformed, and everyone drifts through space as data. However, Lan and MegaMan remain bound by their friendship, and with the help of Trill who makes a surprise appearance, they overcome Cache's trap and return before him. Using CrossFusion, they battle with Cache, but he sends JammingMan duplicates of Lan's friends after him. But with everyone's pleas, Lan and MegaMan are able to build enough strength to overcome the JammingMen and delete Cache.