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.

When Lan wakes up and realizes that his battle with BeastMan and his CrossFusion with MegaMan weren't just a dream, he rushes to SciLab, which is still in shambles from the battle. Lan ends up walking off with a SynchroChip, and it's a good thing he does--ShadeMan starts deleting NetCity, and after MegaMan is unable to stop him, viruses start appearing in the Human World! It's up to Lan and MegaMan to CrossFuse and stop them, but ShadeMan still manages to come out on top. Using the data he stole from NetCity, he fashions a powerful fortress. From there, he plans to strike out at the Human World and drive everyone off the planet!

Ms. Mari's class is going on a field trip to the WaterWorks-main control center for all of the water systems in DenTech City. But there's a problem with the pipes! The nerdiest villain on the Net, BubbleMan, has an evil plan to turn every fixture in the city into a flooding fountain. A Dimensional Area forms around the WaterWorks and BubbleMan materializes to take control of the system. Lan and MegaMan CrossFuse to battle the bubbly bandito, but the power of the Fusion soon fails. Our heroes seem to have a problem communicating--and unless Lan and MegaMan can work together as a team, DenTech City is sunk!!

The Darkloids are at it again! When electrical energy begins to surge all over the city, NetSaver Lan and MegaMan are called in to investigate. They find FlashMan on a dastardly dark mission of blindingly bright madness! His plan? To overload, then drain every circuit in the system! After defeating MegaMan in battle, FlashMan is rewarded with a powerful ""DarkChip"" from ShadeMan and ups the wattage on his rampage. Roll shows up and distracts FlashMan to give MegaMan time to recover, but is quickly overpowered. Just as FlashMan is about to delete MegaMan and Roll, the two unlock a brand new power called ""DoubleSoul,"" and pull the plug on the degenerate Darkloid!

Ms. Mari takes Lan and some of the other kids on a field trip to the ancient Yokayoka Hot Springs, but Lan finds more fun NetBattling a local employee named Tamako. That is, until he discovers Tamako and her NetNavi HeavyMetalMan are so obsessed with NetBattling they won't let Lan do anything else. Even worse, the goofiest villain on the Net, BubbleMan, has returned to get his revenge on MegaMan and Lan, even if it takes opening a Dimensional Area to do it!

A bowling craze is sweeping NetCity, and when Higsby wins bowling tickets, he sees a perfect opportunity to finally take Ms. Mari out on a date. Of course, he needs lots of help from Lan and Maylu just to get the date, and then, worried about embarrassing himself while bowling, he schemes with NumberMan to cheat! But that's far from the worst of it. Infected by a DarkChip, BowlMan starts wrecking the Human World and then even comes to the Human World! Lan and MegaMan CrossFuse and take care of him, but it looks like Higsby's cheating stunt has left him on the outs with Ms. Mari. That is, until she reveals that she'll go on another date with him.

Mr. Match is back in town--but that's the least of Lan's problems! The CyberWorld is being attacked by a flowery fiend with a desire to drain all the Data in DenTech City, and then the world! As computers, traffic systems and just about everything else electronic shuts down, Agent Lan and MegaMan are called into action to figure out how to stop the botanical nightmare, but soon MegaMan becomes trapped by the viney villain VineMan. On a mission of his own, HeatMan suddenly appears and frees MegaMan, but is badly damaged in the battle. As Famous helps Mr. Match recover HeatMan's data, somehow TorchMan's spirit is revived in the process! As MegaMan enters the final showdown with VineMan, he's soon joined by TorchMan to go DoubleSoul and fry the vicious vegetable!!

Lan scores free passes for himself and his friends to check out the new Science and Technology Center before it's Grand Opening. But really, he's been sent there on a secret mission by Mr. Famous to check out a potential virus infection. Little does Lan realize that the virus is a plant by SavageMan and ShadeMan to trap MegaMan in order to exact their revenge, but he sure finds out fast enough. He also learns that, with the DarkChip sent by the Mysterious Man, that revenge expands into the Human World, where viruses and SavageMan himself come after Lan and his friends!

Dex finally returns home from Jawaii Island, where for months he's been in training with the ex-World Three gang to become the ultimate NetBattler. Meanwhile, things are heating up in DenTech City as BurnerMan unleashes a hot blast of chaos throughout the town. The Darkloid has crippled the natural gas system as part of ShadeMan's nasty plan for domination. Lan and MegaMan spring into action, but they're interrupted by Dex and GutsMan--on a mission of their own to try out their new so-called skills. Dex joins forces with Lan to stop BurnerMan's rampage, but only because he wants to defeat Lan himself! Have the old friends become new enemies--or is Dex just dazed and confused?

Someone is illegally giving out DarkChips, the powerful BattleChips that increase a NetNavi's strength but destroy its connection with its NetOp and turn the Navi into a Darkloid. Mr. Famous puts Lan and MegaMan on the trail of the mysterious chips. As the investigation unfolds, Lan and MegaMan have to battle NetNavi SpikeMan, and they also cross paths with a woman who looks just like Ms. Mari--and might be her evil twin sister!

ShadeMan and the Mysterious Man need rare metal to create DarkChips as part of their evil plan to take over the world. But the valuable metal is locked away in a high security building, so they create a Dimensional Area and send in the bumbling BubbleMan to steal it from the safe. When he fails, BurnerMan takes on the task. He completes the mission, delivers the goods to his bosses and prepares for another heist. Meanwhile, Lan and MegaMan spring into action to stop the villains, only to discover that the only way into the Dimensional Area is by CrossFusing at exactly the right moment. But can they perfect the process before all the precious rare metal is pilfered?

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.

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.

Lan can't believe that his dad would give a SynchroChip to Chaud, but that's exactly what Dr. Hikari did. And even worse, he reveals that Chaud and ProtoMan had a stronger CrossFusion than Lan and MegaMan! Lan has to run off on an errand for Maylu, but it turns out that the errand was just a trick by Yai to get Lan, Maylu, Ms. Mari, and Rush into an elevator that turns into a robot and flies them to KingLand. The data from Ayano Tech's latest video-game has been stolen, and it's up to Lan and his friends to get it back!

When Dex does a delivery for Yahoot's curry shop on Jawaii Island, the customer cons him into trading the food for a mysterious box. Yahoot scolds him for not collecting the cash, but soon finds out the seemingly worthless box is actually a powerful NetWrecker machine, capable of altering a NetNavi's data and increasing its power and size to unbeatable proportions! When Lan and the gang land on the island for a visit, he and MegaMan soon find themselves in a NetBattle against Dex and his amazing machine! In his efforts to finally defeat Lan, Dex boosts up GutsMan's power, but he loses control of the big metal ape, sending GutsMan stomping through the streets with Roll as his prisoner. This ""Incredible Guts"" seems unstoppable, and worse yet, nobody knows how to change him back!!

Higsby has put together his very own NetBattle tournament, but it looks like it's going to be a disaster. Only Lan and his friends have entered. Even worse, Shuko, who has a reputation as being so unlucky that she ruins everything around her, wants to enter. Shuko's bad luck starts to affect the others, and she actually wins! But when she goes to cook up the rice she won as the tournament's first prize, she learns that Higsby's power is out. She's sure that she caused the problems, and she's very upset. Looking to cheer her up, her NetNavi SpoutMan goes to the power plant to fix the problem. But when SpoutMan starts crying, cyber water gushes everywhere and threatens to destroy not only the power plant, but also the entire CyberWorld!

Ms. Mari takes Lan and Maylu to an International Exhibition being held at the amazing new Sea Tower building that rises up from the middle of the harbor, but their visit is interruped when ever-ready Net rival Tamako appears and goads Lan into a NetBattle. But soon there's another interruption: SavageMan shows up, sent by the Mysterious Man to take care of MegaMan and Lan in exchange for the DarkChips he craves. The forces of evil aren't messing around this time: they've even sent in Ms. Yuri to destroy the Sea Tower with our heroes inside!

Lan shows up to save a stalled truck on the train tracks, but he finds that a stranger already took care of the situation. Later, Lan meets the stranger, Raika, a NetSaver from Sharo, and his NetNavi, SearchMan, who had helped MegaMan and Lan defeat ShadowMan earlier. Raika is unimpressed by Lan, feeling he relies too much on the SynchroChip and not enough on his intelligence. And when VideoMan attacks, it seems that Raika is right: CrossFusion MegaMan can't defeat VideoMan, but luckily Raika destroys the Dimensional Area generator and gets rid of VideoMan before he can delete CrossFusion MegaMan.

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.

After using the DarkChips too many times, the Darkloids begin to depend on them just to function, so DesertMan breaks into NetPolice headquarters to steal some confiscated DarkChips. Lan and MegaMan rush into action and manage to stop the sandy scoundrel and capture him. Dr. Hikari examines DesertMan and tells the others that he thinks Darkloids might actually be a new digital creation that evolved on its own--unlike every other Navi, which were at least partly created by humans. ShadeMan learns of DesertMan's capture and sends FlashMan to free him, but ShadeMan realizes that FlashMan might need a little help. With the Mysterious Man's assistance, ShadeMan captures Keifer and Manuela and offers to return them in exchange for DesertMan's release.

ShadeMan, who's suspicious of the Mysterious Man, schemes to obtain the DarkChips on his own. Soon after, information on the DarkChips is leaked to Manuela, but when she investigates, she's blocked by a Dimensional Area that surrounds the Secret Warehouse Lab. CrossFusion MegaMan and CrossFusion ProtoMan break through the Dimensional Area's barrier, but they find their way to the chips is blocked by the fearsome GravityMan. Working together, our heroes defeat GravityMan, but they discover, as does ShadeMan, that getting a hold of the elusive DarkChips is much more difficult than they thought.

BubbleMan is convinced that he has the answer to defeating MegaMan: DoubleSoul. The only thing is, true friendship is the basis of DoubleSoul, and BubbleMan has no friends. None of the Darkloids are willing to work with him, so he goes off in search of a Navi that he can trick into becoming his friend. Only he has it all wrong, and thinks that in order to make friends he needs to take data from them. BubbleMan finds SpoutMan and IceMan, and convinces them both to hang out with him, a first step to getting them to give him their allegiance. When MegaMan and the other encounter the odd trio, BubbleMan tricks SpoutMan and IceMan into battling their own friends!

Having gotten a hold of the Darkloids' Dimensional Area generator, SciLab has brought in Dr. Regal to investigate its mysterious energy source. Dr. Regal finds a way to power up the generator, but then a Darkloid named SparkMan shows up and uses the energy of the generator to drain the strength from CrossFusion MegaMan and CrossFusion ProtoMan during a battle! SparkMan succeeds with his mission to destroy the generator, and the secret of its power source comes out--it runs on data from captured NetNavis.

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?

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.