The year is 200X, and everything electronic is connected by internet. In this world, there is no one, rich or poor, who does not own a PET (Personal Terminal), and there is not one PET that does not house a NetNavi, an AI Unit that has the power to delete Viruses and the like. Net Battles (where Operators battle their NetNavis) are popular in this era. That is where Lan Hikari and his NetNavi and best friend, Megaman come in. Striving to become the best NetBattlers, they fight Net Crime and protect the net and real world alike from the likes of the evil terrorist organization the World 3.
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
Darkloid VineMan is attacking all over DenTech City, and he's even trapped Roll in his life-sucking weeds. Mr. Match and HeatMan reappear to help fight, but when HeatMan is damaged, Famous helps in recreating TorchMan. Working with TorchMan, MegaMan creates TorchSoul and burns VineMan to ashes.
BurnerMan returns to steal rare metals so more DarkChips can be built. However, every time he strikes, Lan is too late and can't enter the Dimensional Area he creates. Thus, Dr. Hikari teaches him how to enter Dimensional Areas from the outside. Lan perfects the technique and defeats BurnerMan.
The NetSavers have taken DesertMan hostage, but the Darkloids want him back. SpikeMan kidnaps Keifer and Manuela and threatens to crush them in a car compactor, but Lan and Famous intervene. However, FlashMan then strikes, and deletes DesertMan, but Chaud reappears and defeats him by using a Program Advance within CrossFusion.
Chaud investigates another Darkloid attack involving BubbleMan and BurnerMan, leading him to a hot spring that Lan happens to be visiting. The two work together to stop the Darkloids, leading to a battle beneath the Earth's surface within a lake of magma.
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?
Returning from Kingland, Lan and co. make a detour in Jawaii to visit Dex. Meanwhile, Dex finds a card-scanning device that powers up NetNavis, and he works with the WWW to get his revenge on Lan again. However, the device sends GutsMan rampaging with power (and towering size) through NetCity, taking Roll hostage, King Kong style.
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.
When a vacuum robot sucks up everyone's PETs, Yai and her friends are forced to explore the booby-trapped depths of the Ayano mansion in order to retrieve their stolen NetNavis. Yai's comical and clumsy maid Sakurako makes the excavation more difficult for the cast.
Lan becomes arrogant with his new PET II's powers, so Chaud and Raoul pose as afro wig-wearing villains to teach Lan a lesson. However, SwordMan appears to cause problems, and he overcomes ThunderMan in battle. MegaMan uses ThunderSoul to stop SwordMan.
Dr. Hikari finishes Lan's new PET, the PET II, which amplifies CrossFusion abilities, but the installation isn't completed. However, Dark ProtoMan infiltrates the Sci-Labs to destroy the PET (with MegaMan inside). Anetta takes the PET and Dark ProtoMan gives chase with Chaud close behind to rescue her. Chaud and Anetta work together to capture Dark ProtoMan, but NovaMan appears to finish the job. The installation in PET II is finally completed. Lan appears and, using the PET II, easily deletes NovaMan.
Lan must use his own body in order to help rebuild MegaMan after his PET is damaged beyond repair. Meanwhile, Nebula sends NovaMan, BrightMan, SwordMan, and FridgeMan to attack various locations. In Lan's absence, Raika works with old friend Raoul to stop the invasion. BrightMan is deleted, and the others retreat.
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.
Lan meets Misaki, the first person to test CrossFusion. Misaki uses his NetNavi PrismMan to help in the capture of GravityMan. However, Misaki is overcome with his desire to CrossFuse, and Ms. Yuri uses his desires to lure him toward a trap. Meanwhile, Chaud assists Lan with the Battle Chip Gate to delete GravityMan using the Program Advance.
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.
During a research in Dimensional Core technology, Dr. Hikari becomes trapped in a Jawaiian shopping mall. Lan and his friends break in to rescue him only to find that viruses have appeared in the real world. Fortunately, everyone's NetNavis also substantiate to help rescue Dr. Hikari from the deadliest virus, the LifeVirus.
In order to get a company to sign with BlazeQuest, Chaud finds himself running errands for the company owner named Maeda. The company is working on a new kind of PET technology. One of Maeda's workers decides to steal the data for profit, and ProtoMan must battle with DrillMan to stop him.
Dex's little brother Chisao is visiting from Netopia, but Dex becomes embarrassed when Chisao shows he's a better NetBattler than his big brother. Saburo, a noodle shop owner, gives Chisao his own NetNavi, NoodleMan, and tricks the boy into using him to battle WWW (who runs the curry shop Saburo competes with).
The story is told from a flashback by Masa/Commander Beef. Ms. Mari is love-smitten for Commander Beef, so Higsby, Maysa, and Commander Beef compete for the teacher's heart in a NetBattle tournament. Higsby is defeated early, leaving only Maysa and Commander Beef. Lan fills in for Maysa and battles against Commander Beef's SharkMan
Dr. Regal uses a Dark SynchroChip to fuse with his NetNavi, LaserMan, and then proceeds to rip ShadeMan to shreds. Then, giant-sized LaserMen begin attacking cities throughout the world. Lan uses DoubleSoul during CrossFusion to fight Regal, but it zaps his power. CrossFusion ProtoMan reappears to help fight, but Regal proceeds to attack the Sci-Labs. However, the pleas of the NetNavis' souls (powering the Dimensional Area Converters) revives Lan and he achieves FullSynchro, completely destroying Dr. Regal. With peace restored, everyone watches a night sky of shooting stars, including Ms. Yuri who claims "As one chapter ends, another one begins."
Lan and Chisao are leaving a theme park on a train when SparkMan attacks the train's network. Sal has been tailing the NetNavi and sends WoodMan in to help with MegaMan. In order to delete SparkMan, MegaMan and WoodMan combine their powers to create WoodSoul.
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.
While Lan is away in Sharo, Chaud and Maylu work together to investigate the disappearance of NetNavis who participated in the N1 Grand Prix last year. They meet a robot named Allegro and also re-encounter Kid Grave, now being controlled by Bass. After causing so much trouble, Bass gets rid of Allegro by destroying his CPU, and rejects an offer by Dark ProtoMan to join Nebula.
After having a dream about performing CrossFusion, Maylu wishes to do so and protect Lan for a change. While on a date together at an amusement park, SwordMan attacks and Lan drops his SynchroChip. Maylu picks it up, determined to CrossFuse, but she fails. In the end, Lan saves her again, but their relationship has grown.
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.
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