It's the not-too-distant future, a time when internet technology has swept the world into the Network Age! Everyone carries around a portable communications deviced called a ""PET."" Each PET contains a unique personality program, or NetNavi, that freely navigates the CyberWorld. Lan, an enthusiastic 11-year-old, is introduced to his own, custom-build NetNavi, MegaMan. At first, Lan only wants to use MegaMan to play in cyber NetBattles against his friends' NetNavis. But when computer systems all over town begin to burst into flames, Lan and MegaMan team together to fight against a mysterious criminal syndicate that calls itself World Three!

A robotic cat seems to have its wired crossed as it clamps its jaw onto Dex's calf. Lan and Maylu visit him in the hospital, but are greeted by a less than welcome reception. Meanwhile, Mr. Wily unleashes an electronic rampage of malfunctioning merchandise on DenTech City. Just as Dex is released from the hospital, he's attacked again--this time by a robotic dog! The cyber-pooch escapes, but leads Lan and Maylu on a pursuit that ends on a subway train. Unfortunately, Count Zap and ElecMan have launched a nasty net attack that causes the train to go careening out of control! It's up to Lan and MegaMan to stop the speeding bullet train before it becomes the ""disaster express!""

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?!

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!

At the command of My. Wily, the evil leader of World Three, Maddy, Mr. Match and Count Zap unleash an aquarium full of robotic fish using a unique, jellyfish-type of computer virus. The robot-fish create utter chaos throughout DenTech City. MegaMan and Glide jack into the CyberMatrix to try and stop the virus, but soon find themselves in the path of a ferocious Tidal Wave Virus! Just as MegaMan and Glide are about to be swallowed by the enormous wave, a mysterious NetNavi called SharkMan appears... Is he friend, or foe?

All the water in DenTech City has dried up! World Three has captured Tory and his father Dr. Froid and forced them to use their NetNavi IceMan to freeze the programs that control DenTech City's Waterworks. Lan and his friends rush to save the day, but with MegaMan encased in ice and the Waterworks decaying, can they possibly stop World Three in time to restore the city's water?

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?

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?

The wildly popular TV personality and Yoga master, Yahoot, is in cahoots with World Three! The menacing mystic uses his powerful NetNavi MagicMan to take over the airwaves and hypnotize the devoted viewing audience--turning the entire town into animals! MegaMan jacks in to confront MagicMan, but things get pretty tricky. Our hero is outmatched by the nasty Navi. Just when MegaMan is about to receive the final blow, ProtoMan, controlled by the mysterious champion NetBattler Chaud, comes to his defense, and takes down MagicMan!

Lan and his friends are excitedly training for the upcoming N1 Grand Prix. Unfortunately, the members of World Three have secretly signed up for the competition and Mr. Wily plans to unleash chaos and mayhem at the event. To make matters worse, Higsby's NetNavi, NumberMan, goes berserk while Higsby is trying to upgrade him. Lan and MegaMan rush to the rescue, but it takes them so long to neutralize NumberMan that they almost miss the NetBattle competition! Thanks to Yai and her private jet, Dex, GutsMan, Maylu, Roll, Lan, and MegaMan arrive at the N1 Grand Prix just in time. Dex and GutsMan make a grand entrance at the competition as Chaud issues a challenge to Lan and MegaMan.

The N1 Grand Prix is well under way and Lan's first match is full of surprises! His opponent turns out to be Miyu, the mysterious fortune teller. She uses her powers to predict Lan and MegaMan's every move! Miyu's Navi SkullMan seems unstoppable as he attacks MegaMan with blinding speed. It's going to take a bit more wit and an uncommon usage of BattleChips to beat this bonehead!!

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...?

The N1 Grand Prix rages on, and TorchMan and MegaMan are locked in a heated battle (continued from previous episode)... It seems like MegaMan has the upper hand when Mr. Match downloads a nasty virus to take control of the solar panels on the roof of the Floating Arena's dome. He mercilessly channels the sun's rays into a beam that showers agonizing heat down upon Lan. As MegaMan and Lan suffer the scorching onslaught, Dex, Yai, and Tory jack in their NetNavis to vanquish the viruses one by one. Just as MegaMan's about to become toast, the gang clears the last of the viruses. The Dome opens up, and Lan and MegaMan turn in a blazing victory. Higsby and NumberMan fight the last battle of the day against sweet Sal and WoodMan. Thinking that they can easily defeat the flower girl, Higsby and NumberMan receive an ego smashing as Sal and WoodMan take them out in one blow!

It's time to party! Lan and the gang did so well in their first week in the N1 Grand Prix that Yai invites everyone to a fancy restaurant to celebrate. But when our heroes get to the restaurant, someone is sitting at the table reserved for Yai's family. It's Chaud! Pompous and condescending, it doesn't take long before Chaud insults Yai's family as well as Lan's NetBattling skills. Lan, defending his and Yai's honor, follows Chaud out of the restauraunt and into the night, where he challenges him to a NetBattle. Just as the battle begins, World Three unleashes a hoarde of viruses programmed to delete both MegaMan and Chaud's NetNavi, ProtoMan!

After his brutal battle with Chaud, Lan knows that the only way MegaMan will ever have a chance against ProtoMan is to master the legendary Program Advance technique. Lan recruits Dex to help him as they launch into an impromptu, intensive training course. Meanwhile, WhaleMan and SharkMan are going at it in the main Dome. To give Lan more training time before his upcoming match, Commander Beef holds out until the last possible second before unleashing SharkMan's devastating offense. Lan still can't seem to get it right, but the show must go on. In a ferocious fight with Yahoot and MagicMan, Lan tries the Program Advance once more, this time with better results. He wins the match, but just barely. Chaud and ProtoMan are up next against Count Zap and ElecMan. The World Three nasties pull a cheap trick, but Chaud and ProtoMan tap into the full power of the Program Advance and delete the cheaters from the competition!

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?

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!

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.

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.

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.