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."

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.

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.

BlazeQuest releases new PET models called Progress PETs. Meanwhile, while shooting a commercial for BlazeQuest, Lan meets Inukai, a zookeeper who is abusive to the animals. When Inukai gets in trouble, his frustration attracts Slur, and he is given Asteroid SavageMan to get revenge. Asteroid NetNavis are able to appear in the real world without Dimensional Areas, causing problems with Lan and Chaud, but Dr. Wily helps in the production of a Dimensional Area Generator, allowing the Sci-Labs to create them on command.

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.

While investigating a NetSaver case, Lan notices helicopter pilot Charlie Airstar at the scene of the crimes. Lan presumes Charlie is the culprit, but Charlie is really tracking the true criminal on his own: director of DNN network, Sunayama (and even has the nerve of pursuing Sunayama to Lan's school). Sunayama uses Asteroid DesertMan to fight back, but MegaMan and ProtoMan team up with Charlie's GyroMan to stop him.

Clumsy Yui receives Asteroid StoneMan who gives her the power to turn anything she touches into stone. Panicking, Yui soon transforms the entire business complex and everyone inside into statues. Lan, who is returning an item Yui lost, encounters the problem and battles with StoneMan through Cross Fusion, as Yui had panicked and slotted the Dimensional Chip in.

Lan and Chaud represent BlazeQuest in a car race where NetNavis operate racecars in the real world and get into some comical arguments in the progress. Another participant, Rei Saiko, has mysteriously moved up in the tournament thanks to Rei's new NetNavi, Asteroid FlashMan, who has been cheating in the races. MegaMan and ProtoMan catch FlashMan in the act and are forced to battle with him by Cross Fusing, but Rei escapes before he can be arrested.

Lan and Chaud are led to Netopia to investigate a strange virus disturbance near a research center. There, strange holographic visions of the past appear, and viruses previously believed to be extinct attack in the real world. MegaMan and ProtoMan are also attacked, but they're rescued by a NetNavi named Colonel. After the incident, Chaud receives the Crest of Duo, and he decides to continue investigation in Netopia while Lan returns home.

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.

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.

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.

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.

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.

BubbleMan returns, and this time, he seeks a rare treasure hidden in the depths of the internet. He joins up with IceMan and SpoutMan to undergo this mission, but MegaMan and Roll are close behind to keep the young NetNavis out of trouble. MagnetMan also tails the group, hoping to snag the treasure for himself.

Chaud teams up with Raoul and ThunderMan to investigate missing NetNavis in Netopia. They track the crime down to Ivan Chilliski who was given Asteroid FridgeMan to undergo such crimes. Chaud and Raoul dupe him into revealing himself by posing as the afro-wig villains from Axess, and Chaud uses CrossFusion to battle with FridgeMan.

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.

DarkChips have begun spreading through DenTech City again, so Lan begins an investigation in a factory to catch the culprits distributing the chips. He encounters Inukai and Rei who overcome him in battle. However, Raika reappears, now using CrossFusion to overcome the Neo WWW members.

Lan and Raika investigate the disappearance of ancient weapons being stolen from museums, and Raika suspects that his old friend Iriya may be operating Asteroid JapanMan who is responsible for the crimes. However, Iriya may be innocent when he tries to protect Raika from JapanMan. Lan and Raika delete JapanMan and bring Iriya back to his senses. Before returning home to Sharo, Raika receives the Crest of Duo.