At last MegaMan comes face-to-face with the terrifying Grave VirusBeast that's devouring the entire cyber world... and unless it can be stopped, the network will be destroyed and Mr. Wily will control the world! But it's a losing battle: even AquaCustom Style MegaMan falls before the power of the VirusBeast and is infected with a bug! Then the incredible happens! MegaMan regenerates and emerges in a completely new style: BugStyle! But he gets further infected by the VirusBeast in the process, and now the unstoppable, rampaging monster that's triggering the end of everything is... MegaMan himself!

When a vacuum robot sucks up everyone's PETs, Yai and her friends are forced to explore the booby-trapped depths of the Ayano mansion in order to retrieve their stolen NetNavis. Yai's comical and clumsy maid Sakurako makes the excavation more difficult for the cast.

Maysa and Higsby have both fallen for Ms. Mari, but she's in love with Commander Beef! Higsby challenges the Commander and Maysa to a NetBattle to prove he is the true hero. Meanwhile, Yai and her family manage to build a fantastic stadium for the event in one night, and since Ribitta is stuck somewhere in the Himalayas on assignment, Sal is persuaded to be the announcer at the match. Higsby's up first, but he's so nervous, he loses immediately. Then Lan, NetBattling for Maysa, finally gets to take on his idol, Commander Beef. The love battle is on. Who will have the heart of the shy schoolteacher?

Dex's little brother, Chisao, comes for a visit and our heroes discover the siblings are nothing alike. Chisao attends Kindergarten for geniuses! Chisao idolizes Dex, believing that his big brother is the gang's mentor and leader. Dex begs his friends to play along, just until Chisao returns home to Netopia. Meanwhile, a new noodle restaurant opens up next door to #1 Curry, creating a bitter rivalry between Yahoot and Saburo, the noodle shop owner. Saburo tricks Chisao into helping him sabotage Yahoot's restaurant, and gives him a NetNavi with new powers that stuns even MegaMan! In an explosive NetBattle, Saburo's scheme is uncovered, but when the smoke clears, will Dex remain a hero in his little brother's eyes?

Lan and Chaud are about to have the NetBattle to end all NetBattles, only it ends before it can really start. Chaud is called away on business for his father, so he rushes off to get to a small company to finish a cutting edge new Ultimate Molecular Chip they were hired to create. Chaud soon finds himself doing chores at the company, helping perfect the Molecular Chip, fighting off a hostile takeover of the business, and even defeating the viruses and NetNavi that the company's assistant released after trying to steal the Molecular Chip! What's so great about this chip? What will it be used for? And why is Chaud cleaning bathrooms to help make sure it gets done?

Lan's father, Dr. Hikari, has started an incredible experiment, bridging the CyberWorld to reality! But when things go terribly wrong, and his father goes missing, Lan fears the worst! The key to the experiment, the Dimension Core, has drawn powerful Viruses to it, and now these monsters have materialized in the human world! Lan and his friends must battle these increasingly terrible life-sized Viruses, while MegaMan and the other NetNavis desparately look for a way to help them before it's too late!

Dr. Regal uses a Dark SynchroChip to fuse with his NetNavi, LaserMan, and then proceeds to rip ShadeMan to shreds. Then, giant-sized LaserMen begin attacking cities throughout the world. Lan uses DoubleSoul during CrossFusion to fight Regal, but it zaps his power. CrossFusion ProtoMan reappears to help fight, but Regal proceeds to attack the Sci-Labs. However, the pleas of the NetNavis' souls (powering the Dimensional Area Converters) revives Lan and he achieves FullSynchro, completely destroying Dr. Regal. With peace restored, everyone watches a night sky of shooting stars, including Ms. Yuri who claims "As one chapter ends, another one begins."

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.

Lan and his friends are excitedly training for the upcoming N1 Grand Prix. Unfortunately, the members of World Three have secretly signed up for the competition and Mr. Wily plans to unleash chaos and mayhem at the event. To make matters worse, Higsby's NetNavi, NumberMan, goes berserk while Higsby is trying to upgrade him. Lan and MegaMan rush to the rescue, but it takes them so long to neutralize NumberMan that they almost miss the NetBattle competition! Thanks to Yai and her private jet, Dex, GutsMan, Maylu, Roll, Lan, and MegaMan arrive at the N1 Grand Prix just in time. Dex and GutsMan make a grand entrance at the competition as Chaud issues a challenge to Lan and MegaMan.

Someone is illegally giving out DarkChips, the powerful BattleChips that increase a NetNavi's strength but destroy its connection with its NetOp and turn the Navi into a Darkloid. Mr. Famous puts Lan and MegaMan on the trail of the mysterious chips. As the investigation unfolds, Lan and MegaMan have to battle NetNavi SpikeMan, and they also cross paths with a woman who looks just like Ms. Mari--and might be her evil twin sister!

When film writer Viddy Narcy becomes enraged over the criticism of his latest work, Slur gives him Asteroid VideoMan. With VideoMan's help, Viddy begins painting the city in pink, including part of Lan's face. Lan teams up with Charlie to track Viddy down, and by forming GyroSoul with GyroMan, VideoMan is defeated. But as Viddy escapes, he encounters Sunayama who offers him a position in Neo WWW.

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.

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.

An eccentric guest lecturer, Mr. Higsby, has come to Lan's school. But the lesson he wants to teach isn't on the cirriculum! The nutty professor is on a quest to ""acquire"" all rare BattleChips from those he deems unworthy. His target... Yai. Using his NetNavi, NumberMan, Higsby takes over the school's control system and locks Yai, Ms. Mari, Dex, and Maylu in their classroom, then stages a lopsided NetBattle to obtain his precious prizes. Locked outside, Lan must find a way to send MegaMan to the rescue... before it's too late!

The N1 Grand Prix is well under way and Lan's first match is full of surprises! His opponent turns out to be Miyu, the mysterious fortune teller. She uses her powers to predict Lan and MegaMan's every move! Miyu's Navi SkullMan seems unstoppable as he attacks MegaMan with blinding speed. It's going to take a bit more wit and an uncommon usage of BattleChips to beat this bonehead!!

The girls enter a contest to be just like Aki, a virtual pop singer. However, contestants go missing, so the boys dress as Aki to investigate the situation. A virus has infected Aki causing the mayhem, so MegaMan, GutsMan, and Iceman jack-in to rescue their idol.

The Darkloids are at it again! When electrical energy begins to surge all over the city, NetSaver Lan and MegaMan are called in to investigate. They find FlashMan on a dastardly dark mission of blindingly bright madness! His plan? To overload, then drain every circuit in the system! After defeating MegaMan in battle, FlashMan is rewarded with a powerful ""DarkChip"" from ShadeMan and ups the wattage on his rampage. Roll shows up and distracts FlashMan to give MegaMan time to recover, but is quickly overpowered. Just as FlashMan is about to delete MegaMan and Roll, the two unlock a brand new power called ""DoubleSoul,"" and pull the plug on the degenerate Darkloid!

ShadeMan and the Mysterious Man need rare metal to create DarkChips as part of their evil plan to take over the world. But the valuable metal is locked away in a high security building, so they create a Dimensional Area and send in the bumbling BubbleMan to steal it from the safe. When he fails, BurnerMan takes on the task. He completes the mission, delivers the goods to his bosses and prepares for another heist. Meanwhile, Lan and MegaMan spring into action to stop the villains, only to discover that the only way into the Dimensional Area is by CrossFusing at exactly the right moment. But can they perfect the process before all the precious rare metal is pilfered?

Lan and Chaud travel to Nebula's base where Anetta is being held hostage. Once there, however, ShadeMan materializes in the real world and they battle with him using Cross Fusion. The ship in which the base is being held on is going to explode, so Lan and Chaud need to evacuate... but in the cyber world, ShadeMan is fighting with MegaMan and ProtoMan. Chaud is tempted with a DarkChip to rescue ProtoMan from deletion, but will he use it?

Mameo, a boy attending Lan's school, hates vegetables. Slur targets him and gives him Asteroid VineMan who can help destroy all of the vegetables in the world. This enrages Lan since vegetables are a prominent ingredient in curry, so Lan and Chaud track Mameo down. However, VineMan turns on Mameo, so Lan and Chaud must rescue him from his own NetNavi.

Inukai begins an attack by transforming automobiles throughout DenTech City into wild animals. Lan and Famous investigate the situation and MegaMan goes to battle with SavageMan but encounters all four Neo WWW NetNavis at once. Colonel reappears and rescues MegaMan in the end.

Lan meets Route, a guide program at an automobiles museum. Meanwhile, criminal Ken has to steal cars in order to rescue his girlfriend from a mob leader, and he is given Asteroid BrightMan to do so. Lan intervenes but is overpowered by BrightMan, so Route sacrifices herself in order to help defeat the Asteroid. However, Route is revived from back-up data, and peace is temporarily restored.

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.

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.

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.