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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.