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.

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.