Seasons & episodes

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.

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 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.

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.