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!

Lan, Maylu and Chisao visit the Sci-Labs and witness Dr. Hikari's latest experiment in Dimensional Area technology—CrossFusion, the merger of a NetOp with his/her NetNavi, but the CrossFusion makes a NetOp lose his strength. However, the laboratory is attacked by real-world viruses and the Darkloid NetNavi SavageMan. Lan has no choice but to perform CrossFusion himself and stop SavageMan. After beating SavageMan, Lan passes out, but recovers a few seconds later.

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.

BubbleMan, who was frozen in cyber space by Colonel, finds himself freed when a strange energy appears before him. Left behind is an infant NetNavi. He carries it to NetCity before collapsing and being found by Roll and the others. Meanwhile, strange disturbances appear in the real world as two gigantic cloaked beasts begin battling. Lan, Chaud, and Raika intervene, and the beasts move their battle to the internet. When MegaMan battles with them, the infant's power combines with his own, and MegaMan defeats the beasts using two new styles modeled after the beasts.

Lan struggles with the memories of Beyondard, but everyone becomes well-adjusted to returning home. Peace isn't maintained for long, however, when strange cyber weeds appear all over a factory in Sharo, and Raika is forced to deal with substantiated viruses. The same thing soon occurs in DenTech City, and upon the defeat of the viruses, Lan faces a strange humanoid being with long blond hair.

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!

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!

Lan finds a warehouse full of DarkChips, and he starts to think he's the best NetSaver on Earth. He's sure that it'll be easy for him to find the factory that's making the DarkChips. Meanwhile, Chaud has plans of his own to find the factory: he follows Ms. Yuri. At the warehouse, Lan stumbles upon the factory and also upon DesertMan, who's so powerful that Lan and MegaMan can't defeat him. Just when it seems that it's curtains for them, CrossFusion ProtoMan shows up and helps to save the day.

Raika and Lan are instructed to work together to investigate what's apparently a ghost that's robbing banks and corporations. Unable to get along with each other, they decide to work independently. When the ringleader behind the thefts turns out to be DesertMan (who can make himself invisible), MegaMan finds himself in big trouble and facing a tough NetBattle all alone. Meanwhile SearchMan, against Raika's orders, goes in to rescue MegaMan. Raika is shocked that SearchMan has disobeyed his orders. MegaMan gains a new DoubleSoul power, Search Soul, and with it, he defeats DesertMan.

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.

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.

Zoano SnakeMan and Zoano GutsMan are subdued, but Zoano DarkMan is issued to capture Trill himself. The heroes are overwhelmed by his power, but Iris's NetNavi is able to assist in the protection of Trill, and she carefully houses him within Iris's PET. However, upon appearing in the real world with a CopyBot, DarkMan captures Iris and uses a device that opens a portal to Beyondard in the real world, and Lan, Chaud, Raika, Dingo, and Maylu are transported there with him.

While searching for ingredients for Pat's curry, Dingo and Trill encounter DiveMan and follow him to a nearby lake castle. Inside, they discover that two humans, Captain Blackbeard and Yuika, are cooperating with Zoano DarkMan and have taken Iris prisoner. Dingo and Trill infiltrate the castle in hopes of rescuing Iris, but they must battle with Yuika's NetNavi, CircusMan. In the end, Iris is rescued.

Moliarty and Press somehow become separated from Beyondard and appear in DenTech City, and they begin excavating holes throughout the city, unaware of the damage they're inflicting. Lan is sent to investigate the disturbance and believes them to be enemies, so MegaMan battles with GroundMan. However, Maylu, Chaud, and their respective Navis rush to the scene to clear their names.

Maylu is excited about purchasing a trendy new handbag, and she drags Lan along for the ride. Meanwhile, one of BubbleMan's miniature CopyBots is unintentionally stolen, and he chases across DenTech City to retrieve one. When he mistakens the CopyBot for being inside Maylu's handbag, he steals it, forcing an enraged Maylu to chase after him.

No one knows what to make of the mysterious new NetNavi Bass, but everyone is intruiged when it seems that he alone can resist the CyberBeast that's slowly destroying the entire Cyber Network! What will he do with that kind of power? What does he want? And whose side is he on: MegaMan's? Grave's? Taking no chances, Kid Grave sends FreezeMan to delete Bass. Then Bass makes off with an unconscious MegaMan, launching Lan and his friends on a desparate search to find him. And worst of all: Mr. Wily has returned.

The NetSavers and Lan's friends have devised a plan to bring ProtoMan back from the darkness with a VaccineChip. Luring him into a trap at a deserted hotel, the plan is put into motion, but the chip fails. Chaud performs CrossFusion with Dark ProtoMan to try and cure him, sending the two into a world of memories where they battle with the darkness. The darkness is eventually alleviated, but Chaud and ProtoMan are both hospitalized after the battle.

Thirty years ago, Duo's comet had crashed on Earth, and Dr. Regal plans to travel through space and time to absorb its power. MegaMan, ProtoMan, SearchMan, and Colonel rush through time to thwart Dark MegaMan who was sent to help Dr. Regal gain access to the comet. However, Dark MegaMan plans to absorb the power himself and become the ultimate NetNavi, but Slur refuses to allow him to do so by deleting him. Before fading away, Dark MegaMan self-destructs and prevents Dr. Regal from succeeding. The heroes return home, and the renmants of Dark MegaMan's being rejoin with MegaMan's soul, and MegaMan forgives him.

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 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.

All contact with NetNavis in DenTech City's moon station has been lost! While Commander Beef rockets to the moon to investigate, Lan and his friends are trying to learn more about the mysterious new ""ExtraCodes"" rumored to make NetNavis mightier than ever! Then Commander Beef encounters a dangerous new NetNavi, PlanetMan, who's trying to take over the moon. But before the Commander can react he's locked outside the lunar station with only two hours of air left! With Mr. Famous's help, Lan and his friends rush to the space center and beam MegaMan and GutsMan to the moon's cyber station to battle PlanetMan. But even with MegaMan now wielding an ExtraCode to get the amazing AquaCustom Style, will he be able to handle its awesome, energy-draining power?

AyanoTech is hosting a NetMobile Grand Prix in NetCity! MegaMan and his friends, plus World Three and the Net Agents, all compete to see who has the fastest NetVehicle! But the winning car will have to be more than just speedy, because in this race, anything goes, including using BattleChips to sideline your opponents. It's all legal! And, as if driving under those conditions weren't tricky enough, the CutMan Brothers, who vowed to take revenge against MegaMan, join the race and create utter mayhem! In all the confusion, who will take the lead and win?!

The Air Show Festival has arrived! Lan and MegaMan would like to enjoy it, but a Cyber World villain-for-hire named ShadowMan has been brought in by the Mysterious Man to destroy the Control X traffic management systems around the world, and that includes the new one controlling the Air Show. When MegaMan swings into action, he discovers a hard-hearted fellow NetNavi called SearchMan who is also after ShadowMan. And SearchMan is perfectly willing to delete anything in his way--even MegaMan.

VideoMan tricks MegaMan into coming to a video store and then records his movements and copies his image. VideoMan then transfers MegaMan's likeness to videotapes around the world so that every time someone watches one, the MegaMan copy appears and causes trouble. Lan and Chaud finally figure out how to erase the tapes using a magnetic field, and as CrossFusion MegaMan and CrossFusion ProtoMan, they erase all the MegaMan copies and delete VideoMan as well.

When Maylu receives a new kitten, Rush feels neglected and runs away on the internet. He befriends a Maloko sheep virus, but BubbleMan is causing electrical interference throughout the city in hopes of reviving ShadeMan. Rush and the Maloko intervene.