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.

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.

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.

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.

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.