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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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?

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.

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!

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?

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.

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.

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.

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.

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.