A mysterious young girl named Yai transfers into Lan's 5th Grade class. Impressed by her incredible wealth, Lan and Dex unwittingly find themselves trapped on the prococious little girl's estate. All the while, Maddy (an agent for World Three) and her maniacal NetNavi, WackoMan, unleash a devastating computer virus that causes the traffic lights in DenTech City to go haywire, creating an enormous traffic jam throughout the city! Lan jacks his PET into a traffic signal control computer, and discovers that the traffic management center has been infected by a computer virus. Will Lan and MegaMan be able to stop the panic?!

World Three's Count Zap is on a robbing rampage, only no one knows that his real target is the videogame that AyanoTech is about to release; if he can steal that, he'll make kids all over the world miserable. Lan and his friends learn of the sinister plot, and MegaMan goes up against ElecMan to stop it. But even with the help from Black Rose and WoodMan, will MegaMan be able to stop the ultra-powerful ElecMan?

Just before their Net Battle competition at the N1 Grand Prix, Maddy insults Maylu and Yai in the trendy Souvenir Shop. Maylu vows right then and there to beat Maddy and her NetNavi, WackoMan, in their upcoming match. Unfortunately, during the NetBattle, WackoMan proves that he's as much a cheater as Maddy. But just when it looks like Roll is going to be defeated, Maddy makes a critical mistake and Roll seizes the moment! Meanwhile, Lan and MegaMan take on Mr. Match and TorchMan. Like Maddy, Mr. Match hatches a diabolical scheme to trick Lan into losing the match. Will World Three succeed in defeating the best Navis in the N1 Grand Prix...?

Disguised as Higsby, Yahoot gives Maylu an evil BattleChip, which she uses in her team match with Lan--against Mr. Match and Maddy. This ""twisted chip"" has now taken over her PET and put Roll under the control of Count Zap and World Three! Every time Lan sends MegaMan into action, Roll, now calling herself Empress, steps in his path and attacks our blue hero! Finally the real Higsby appears and tells Maylu the secret to stopping Roll from her rage. With Roll back to normal, Lan and Maylu easily win the match. Up next, Chaud and ProtoMan are teamed up with a teen NetBattler and his singing NetNavi, ShiningMan--against WhaleMan and RocketMan. Not exactly team players, Chaud and ProtoMan take out their opponents and ShiningMan in one blow!

In order to revive MegaMan, his back-up frame must be retrieved from the SciLab network. However, PharaohMan has taken over the network and turned it into a barren desert wasteland. Roll and the other NetNavis jack-in to retrieve the frame, but PharaohMan intervenes.

Lan's bus breaks down while driving through Kingland, so he visits a nearby mansion. It's actually the home of Count Zap who has been persuaded by his mother, Mama Zap, to get revenge on Lan for destroying the WWW. Count Zap traps Lan in a NetBattle where he's shocked every time MegaMan takes damage. Meanwhile, Mr. Match mistakes the planes and goes to country where everyone knows about curry.

The mysterious Bass floats over NetCity, watching as the Grave VirusBeast rampages on the loose, devouring NetNavis and growing in size! Even with ProtoMan's help, Lan and MegaMan are powerless to stop the Beast from swallowing their friends! Can anything be done to halt this monster before it consumes the entire cyber network? What role does the cryptic Bass have to play?!