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.

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.

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.

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.

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.

Lan and his friends' NetNavis disappear in a tornado of wind, and they track them to Shiisaa Island. There, they meet Lily and her NetNavi WindBlastMan. Ms. Yuri also appears on the island, hoping to steal the data within an ancient relic. When SpikeMan disrupts the relic, a huge storm brews over the island, and using WindSoul MegaMan defeats Spikeman.

A Dimensional Area has appeared over a factory in Sharo, so Raika calls for Lan to help infiltrate it against his general's orders. Inside, they meet FridgeMan who is trying to steal minerals. Upon his defeat, Lan learns that Raika was mostly trying to rescue his pet dog that was trapped in the factory.

An elderly man named Tensuke wishes to better connect with his grandson who cares more about NetBattling, not Tensuke's love for tops. Lan and Maylu decide to help Tensuke perfect his NetBattling skills with NetNavi TopMan.

Revived, ShadeMan plans to get revenge on Dr. Regal. First, he captures Rush and uses his technology to appear in the real world without the aid of a Dimensional Area. He goes on a rampage through DenTech City to find Dr. Regal, but Lan intervenes. However, once Dr. Regal appears, he unveils a tower of Dimensional Area Converters and covers the entire planet.

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!

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?

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!

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.

A girl named Anetta lost her NetNavi in the past, and she's lead to believe that Chaud's ProtoMan was the one who deleted her. She works with Ms. Yuri and the Darkloids to try and infect ProtoMan with a DarkChip, but will she succeed?

Chaud is having trouble dealing with the loss of ProtoMan to darkness, but Lan helps comfort him with his loss. Later, when GravityMan and ProtoMan attack, Chaud is forced to fight against his own NetNavi to protect important NetSaver data while Lan handles GravityMan.

Yai needs her friends' help again. An AyanoTech satellite has been covered in space debris, so Lan and co. board a space station built from junk to solve the problem. In the station's network, MegaMan meets JunkDataMan, the NetNavi responsible for the mess, and a misunderstanding leads to a battle between the two.

The NetAgents have returned to DenTech City, and Lan is shocked to learn that everyone already knew their identities were Sal, Miyu, and Maysa. Mr. Gauss also returns to town to make a deal with Ms. Yuri, but mistakening Ms. Mari for her, he holds her hostage. Commander Beef dashes to rescue his love from danger.

Misaki uses the power of a Dark SynchroChip to CrossFuse, but as a side-effect, his human heart is enriched with darkness. Captured by the NetSavers, they begin to heal him, but Ms. Yuri reinstitutes his darkness, causing him to escape. Lan battles with Misaki in CrossFusion, but the battle causes Lan's PET to be badly damaged.