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?

2 on 2 battles continue: MegaMan and SharkMan (Commander Beef) vs. StoneMan and BlasterMan. StoneMan and BlasterMan open a hole in the arena, and the four NetNavis are quickly sucked out of the ring and into a cyber world. They have 10 minutes to return to the ring, or they will be disqualified. Finally, MegaMan and BlasterMan return, and MegaMan is victorious. But Lan suspects that Commander Beef is Maysa in disguise.

The N1 Grand Prix moves into a special, second round of Tag Team competition when it is announced that two teams, which had previously been eliminated, can now re-enter the games. The two lucky teams are chosen by a computerized wildcard, but World Three rigs the competition so that Mr. Match and Maddy are selected, pitting TorchMan and WackoMan against MegaMan and Roll. Neither Lan nor Maylu are nervous about the match-ups since they have beaten these opponents before. However, both our heroes are in for a frightening surprise when World Three tricks Maylu into downloading a special BattleChip that transforms Roll into an evil NetNavi! The newly transformed ""Empress"" immediately launches a vicious attack against MegaMan. Will she succeed in finally deleting him?

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

The match begins. Chaud insists on working alone, so he takes on BlasterMan and StoneMan single-handedly. BlasterMan is deleted, but StoneMan has a regenerative core that makes him difficult to delete. However, ProtoMan becomes overcome when Chaud realizes he lost the chips needed for the Program Advance in the elevator shaft with Yai.

At long last the waiting is over! The Championship Battle of the N1 Grand Prix has finally arrived, and the contestants are Lan and Chaud with their NetNavis MegaMan and ProtoMan! But as the teams clash in a dramatic battle, they unleash so much power that the hydraulic support beams holding up the Floating Arena are damaged and the arena starts sinking! While the terrified crowd evacuates, the gang realizes that Lan and Chaud are continuing their heated battle--and both plan to battle to the end, even if it means going down with the arena! While the gang watches from afar, Lan and Chaud's NetBattle climaxes with a never-before-seen Double Advance! As the crowd cheers, the energy the titanic Double Advance unleashes a powerful and malevolent NetNavi from his secret tomb. PharaohMan is released back into the world!

PharaohMan has returned, and he's back with a vengeance! Mr. Wily sends an army of StoneMan and BlasterMan clones to capture the NetNavi, but PharaohMan has plans of his own. Meanwhile, Lan gets a shock: Chaud actually feels bad about MegaMan being deleted and offers to help him! But maybe MegaMan isn't gone after all, since Lan and his friends find strange data on their PET's. While they try to figure out how to rebuild MegaMan, PharaohMan, angry because he was imprisoned for twenty years and had his ""kingdom"" taken from him, uses the Cyber Network to cause disasters in the real world. And then, Lan's father shows up to help Lan and his friends--surely he can bring MegaMan back.

The BlasterMan/StoneMan clones attack PharaohMan, but he escapes unscathed. Roll and the others are not so lucky and are turned to stone by PharaohMan. As this part of the Cyber Net begins to collapse, ProtoMan succeeds in saving MegaMan's frame. SharkMan, SkullMan, and WoodMan work at shutting down SciLab's main computer, while ProtoMan takes on PharaohMan single-handedly. Just when it seems ProtoMan will be deleted, MegaMan returns and the two NetNavis attack PharaohMan with the Double Program Advance. BlasterMan and StoneMan reappear and take the weakened PharaohMan to Mr. Wily at World Three Headquarters. MegaMan follows them but is immediately set upon by BlasterMan and StoneMan, so Lan engages MegaMan's new ability, StyleChange, which allows MegaMan to easily defeat the Solo NetNavis. In the end, Mr. Wily and PharaohMan's showdown of wills ends in the destruction of World Three Headquarters.

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.

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.

While in Brand City, Lan sees a purse he'd like to buy for his mother, but it's too expensive. He learns of an underground NetBattle game where he can win the purse, but it's really a trap set up by Ms. Millionaire to capture NetNavis for her own personal museum. Meanwhile, Mr. Match arrives to Netopia's Heaven City, but he's too late again: Lan left Netopia's Heaven City.

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.

Lan's last venture of his vacation is to try all kinds of different curry—his favorite food. WWW members Mr. Match, Maddy, Count Zap, and Yahoot reunite to trap Lan during his all-you-can-eat curry buffet, but Lan's own friends make a surprise turn to help take the WWW down.

Back home, Lan is introduced to NetCity, an online city for NetNavis to interact in. Meanwhile, a NetNavi named AirMan traps Yai in her bathroom and fills it with hot steam. MegaMan goes to stop the NetNavi who claims to be a member of Grave, a new net-crime syndicate.

A strange acid rain and viruses loom over NetCity, destroying it. MegaMan and co. jack-in to fend off the viruses, and they soon discover an underground factory that's the source of the mayhem. But when MegaMan goes to destroy it, he meets ShadowMan, an assassin NetNavi hired to delete him.

Mysteriously, Higsby has become very wealthy, and Yai's family has gone broke. Mr. Gauss is responsible, a member of Grave who is using MagnetMan to switch people's bank accounts around. Lan and Chaud investigate the situation, but Gauss escapes.

Sal takes the kids on a camping trip into Okudan Valley. There, she meets a childhood friend Dave. But Dave claims to be a Grave member who plans to use QuickMan to destroy the valley's dam. It turns out to be a bluff but CutMan, another Grave member, appears to finish the job.

A new air-conditioning penguin toy is introduced during a heat wave, but they're really being distributed by Grave. Soon, the penguins begin to blanket DenTech City under a sheet of ice. Lan manages to jack-in to NetCity and finds that FreezeMan is responsible for this mess. FreezeMan is defeated with the help of another new NetNavi named HeatMan.

The events of episodes 33 and 36 are recapped through the point-of-view of the WWW. This episode elaborates on the deletion of TorchMan to the hands of FreezeMan, and the rebirth of TorchMan in the form of HeatMan thanks to the efforts of the enigmatic man named Famous.

The five younger brothers of CutMan declare revenge against MegaMan for deleting their older brother. Luring MegaMan into a fake China Town district, they begin attacking with a barrage of origami warriors. ProtoMan appears and assists in the rescue of MegaMan.

Lan meets a boy named Whip, unaware that he's really the princess of Brightland, Princess Pride. ShadowMan targets Pride because her NetNavi, KnightMan, has a valuable virus protection program. Lan and MegaMan aid "Whip" in the battle against ShadowMan.

Tora, world-class NetChess Battling Champion and his NetNavi KingMan, have come to DenTech City to challenge Lan and MegaMan. Tora never plays for free though, and demands that whoever loses the NetBattle must give their NetNavi to the winner! Lan accepts the challenge, but soon realizes he has no idea how to play chess! Luckily, Maylu does and partners up with Lan. As the incredible battle nears its end, ShadowMan mysteriously appears on a mission to delete both KingMan and MegaMan!

All of the NetNavis in DenTech City are turning into cats! A freak electrical storm released a Cat Virus that's causing the transformations. To add to the confusion, Rush has somehow materialized in the human world. Dr. Hikari shows up to lend his help, and he reveals that if the Cat Virus isn't stopped soon, MegaMan and the others will remain cats forever! After sixty-foot-tall versions of Rush and the Cat Virus face off in the human world, MegaMan and the others are able to defeat the Cat Virus and give Dr. Hikari the data he needs to write a vaccine program. Everything goes back to normal--except that Rush can still appear in the human world. Will the vaccine work? And why is Rush now suddenly able to appear in the human world whenever he wants? What is going on?

Maddy is bored and restless since the disintigration of World Three, so she jumps on the offer to become Mr. Gauss's new executive assistant--despite protests from her old companions. Meanwhile, Commander Beef gets wind of a secret meeting for senior Grave officers which is to take place at Gauss's mansion. He, Lan, and the others crash Gauss's costume party, unaware that it is actually a ruse to lure them into his trap. When Gauss traps them in the basement of his mansion and begins flooding it, Lan tries to save himself and his friends by jacking into the net while fighting rising waters. In order to pull the plug on the rising water, MegaMan must battle MagnetMan. Watching the drama unfold, Maddy begins questioning Grave's ruthless and controlling methods and decides to aid Lan, lending WackoMan's support to MegaMan in a mad NetBattle against MagnetMan. In the end, Maddy realizes that she's happier back with her old friends--even if it means washing dishes back at #1 Curry!

Kyuta, a new student in Lan's class, is the son of famous baseball player Kyuma Hoshida, but he's depressed about having to move from his old town. To cheer him up, Lan and all of his friends in DenTech City invite him to a game of NetBaseball.