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!

Feeling like he's lost his inner fire, Mr. Match decides the only way to ignite it again is by defeating MegaMan once and for all. To lure him into his high-temperature trap, Mr. Match sends TorchMan out on a spree of overheating chaos throughout DenTech City. Maylu happens to be at the salon at the time, her hair gets fried, and Lan makes the mistake of laughing at her. Meanwhile, MegaMan hasn't replied to TorchMan's mayhem, causing Mr. Match to grow impatient. He sends TorchMan to challenge MegaMan directly, but the message stops at Roll, who also happens to be mad at MegaMan! Maylu and Roll decide to take on TorchMan, falling right into the terrible trap. Will MegaMan show up before Roll gets toasted?

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...?

Schoolmates Maylu and Tory, with their NetNavis, Roll and IceMan, battle it out in Week Two of the N1 Grand Prix! After Roll defeats IceMan, the games shift to a more challenging event: the Tag Team Matches, as pairs of NetNavis battle each other. First up, the mysterious StoneMan and BlasterMan challenge GutsMan and WoodMan. By the end of the match, it's revealed that StoneMan and BlasterMan are actually Mr. Wily's secret weapons. The two are revealed to be Solo NetNavis, which means they have free will and can battle without NetOps! After soundly defeating GutsMan and WoodMan, the two Solo NetNavis set their sights on MegaMan and SharkMan! With the undefeated StoneMan and BlasterMan at his side, will Mr. Wily succeed in finding the NetNavi with the Ultimate Program?

It's the semi-finals at the N1 Grand Prix and MegaMan and Lan are teamed up with ProtoMan and Chaud against the Solo NetNavis, StoneMan and BlasterMan. Before the match, Chaud gets stuck in an elevator with Yai, but makes it back to the arena just in time. As the match begins, MegaMan is temporarily taken out of the battle by ProtoMan who then faces off against BlasterMan, and literally blows him away. MegaMan gets back in the action, but StoneMan buries him under a ton of viruses. Barely missing a beat, Chaud sends ProtoMan in to finish the job and blows StoneMan to pieces. But StoneMan has a regenerative program that allows the brute to pull himself back together again! Lan tells Chaud to use the Program Advance, but Chaud can't because he lost two critical BattleChips while saving Yai in the elevator incident. MegaMan returns and he and Lan unleash the Program Advance, taking StoneMan down. Now, it's on to the finals, where MegaMan and ProtoMan face off for the title of N1 Grand Pri

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 visits Netopia's Heaven City, but as soon as he arrives, his PET is stolen. After chasing the thieves down, he befriends a man named Raoul with NetNavi ThunderMan. Meanwhile, the mayor of Heaven City has plans to bulldoze Raoul's downtown home, but Lan agrees to help fight back. Meanwhile, Mr. Match arrives to Jawaii islands to have a rematch with Lan, but he arrives too late: Lan left Jawaii islands.