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.

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.

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!

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.

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.

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.

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?!

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.

With the help of Yai and his friends, Lan blasts off to space to stop Dr. Regal against the NetSavers' orders. JunkDataMan also reappears to help the kids by giving MegaMan JunkDataSoul to clear the space of junk. When Lan reaches the station, he's instead confronted by Dark ProtoMan, and after the battle, the space station sends on a crash-course to Earth. However, JunkDataMan is able to rescue the children at the last moment.

The CrossFusion Members continue to deal with the Zoanoroid threat in DenTech City. Meanwhile, many Beyondard residents attempt to fight back against Wily but all fall short. In the end, in order to defeat Wily, Trill and MegaMan combine their powers and Lan performs Cross Fusion, merging into a new "Juuka Style." With this ultimate power, Lan is able to destroy Wily and close the portals between both worlds. With peace restored, Lan and his friends return home, but not before saying goodbye to new friends Trill and Iris.

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!

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.

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.

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!

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.

The Grave VirusBeast continues absorbing the internet. Lan and his friends team up with former WWW members to try and stop Grave. However, Mr. Gauss and MagnetMan intervene, and a strange bug left behind by Bass in MegaMan's system begins to consume him. Meanwhile, Bass attempts to absorb the VirusBeast, but is himself absorbed instead.

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.

BubbleMan becomes a pawn in the power struggle between ShadeMan and the Mysterious Man. Meanwhile, the Mysterious Man sends BurnerMan on a mission to cause a devastating volcanic eruption. The site happens to be right under the hot springs Lan and the gang have gone to for vacation. As the tiny town begins heating up and melting down, Chaud joins Lan to stop BurnerMan from superheating the magma deep below the earth and causing massive molten mayhem. But can the NetSavers stop their fiery foe in time?

MegaMan tries to offer comfort to Chaud, who has just lost his NetNavi ProtoMan. Meanwhile, Lan is asked to stand guard at a fashion show that shows off special new holographic technology. Maylu is also there, but things turn for the worse when Yuri tries to steal the technology. SparkMan appears to help her with her mission, but Chaud also arrives to stop Yuri himself.