Seasons & episodes

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.

While on summer vacation, Lan and Maylu search around the world for a beetle and find themselves in ancient desert ruins. There, they find a magic lamp that summons MistMan, a NetNavi genie, but Ms. Yuri, SwordMan, and FridgeMan also seek the power of MistMan. In the end, MistMan is freed and helps MegaMan in deleting both SwordMan and FridgeMan.

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.

Using Control X, the NetSavers plan to locate Dr. Regal's hidden space hideout. But to stop their plan, Nebula sends an army of previously-deleted Darkloids after the program. MegaMan, SearchMan, and the NetPolice re-delete the Darkloids while Dark ProtoMan goes straight for the program that Chaud and Anetta are working with. Meanwhile, Bass appears and revives ShadeMan.

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.

When Ms. Mari witnesses the apparent death of Ms. Yuri, she reveals the truth about her twin sister that she was separated from at a young age. However, Ms. Yuri returns to life and is ordered to kill her sister. She takes Misaki hostage and reveals that she's a superhuman descendant of Duo, an intergalactic force that will soon arrive on Earth. Lan and the kids intervene and try to stop Ms. Yuri who uses a Dark SynchroChip to fight, but she is swayed against Nebula. In the end, Dark ProtoMan appears and strikes, presumably killing both Ms. Yuri and Misaki.

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.

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.

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."

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.

ProtoMan arrives to help ward off Bass, but more giant-sized viruses continue appearing in the real world. Lan and Chaud prepare to send their NetNavis to the comet, but Bass intervenes in hopes of overcoming the power that threatens Earth himself. Bass meets Slur who swiftly defeats him. Slur is a subordinate of Duo, an intergalactic force threatening to erase Earth after Dr. Regal's activity with darkness. However, Lan and Chaud convince him to spare their planet, and Duo challenges them to prove humankind's worth. After the incident, Lan receives a marking on the palm of his hand, the Crest of Duo.

BlazeQuest releases new PET models called Progress PETs. Meanwhile, while shooting a commercial for BlazeQuest, Lan meets Inukai, a zookeeper who is abusive to the animals. When Inukai gets in trouble, his frustration attracts Slur, and he is given Asteroid SavageMan to get revenge. Asteroid NetNavis are able to appear in the real world without Dimensional Areas, causing problems with Lan and Chaud, but Dr. Wily helps in the production of a Dimensional Area Generator, allowing the Sci-Labs to create them on command.

Mameo, a boy attending Lan's school, hates vegetables. Slur targets him and gives him Asteroid VineMan who can help destroy all of the vegetables in the world. This enrages Lan since vegetables are a prominent ingredient in curry, so Lan and Chaud track Mameo down. However, VineMan turns on Mameo, so Lan and Chaud must rescue him from his own NetNavi.

While investigating a NetSaver case, Lan notices helicopter pilot Charlie Airstar at the scene of the crimes. Lan presumes Charlie is the culprit, but Charlie is really tracking the true criminal on his own: director of DNN network, Sunayama (and even has the nerve of pursuing Sunayama to Lan's school). Sunayama uses Asteroid DesertMan to fight back, but MegaMan and ProtoMan team up with Charlie's GyroMan to stop him.

Clumsy Yui receives Asteroid StoneMan who gives her the power to turn anything she touches into stone. Panicking, Yui soon transforms the entire business complex and everyone inside into statues. Lan, who is returning an item Yui lost, encounters the problem and battles with StoneMan through Cross Fusion, as Yui had panicked and slotted the Dimensional Chip in.

Lan and Chaud represent BlazeQuest in a car race where NetNavis operate racecars in the real world and get into some comical arguments in the progress. Another participant, Rei Saiko, has mysteriously moved up in the tournament thanks to Rei's new NetNavi, Asteroid FlashMan, who has been cheating in the races. MegaMan and ProtoMan catch FlashMan in the act and are forced to battle with him by Cross Fusing, but Rei escapes before he can be arrested.

Lan and Chaud are led to Netopia to investigate a strange virus disturbance near a research center. There, strange holographic visions of the past appear, and viruses previously believed to be extinct attack in the real world. MegaMan and ProtoMan are also attacked, but they're rescued by a NetNavi named Colonel. After the incident, Chaud receives the Crest of Duo, and he decides to continue investigation in Netopia while Lan returns home.

Mr. Gauss's daughter Tesla announces the formation of a new net-crime syndicate called Neo WWW, and their first mission is to rescue the imprisoned Mr. Gauss. Lan and the NetSavers attempt to intervene, but with the aid of Inukai, Rei, and Sunayama who have all joined Tesla, Mr. Gauss is rescued and Tesla becomes the new operator of MagnetMan.

When film writer Viddy Narcy becomes enraged over the criticism of his latest work, Slur gives him Asteroid VideoMan. With VideoMan's help, Viddy begins painting the city in pink, including part of Lan's face. Lan teams up with Charlie to track Viddy down, and by forming GyroSoul with GyroMan, VideoMan is defeated. But as Viddy escapes, he encounters Sunayama who offers him a position in Neo WWW.

Inukai begins an attack by transforming automobiles throughout DenTech City into wild animals. Lan and Famous investigate the situation and MegaMan goes to battle with SavageMan but encounters all four Neo WWW NetNavis at once. Colonel reappears and rescues MegaMan in the end.

While visiting Dex in Jawaii, Lan meets Dingo, a fellow lover of curry. The two become quick rivals and Lan challenges him to a NetBattle with TomahawkMan. Meanwhile, Viddy plans to bury the entire island in a giant wave of curry sauce, so Lan and Dingo infiltrate his giant fish airship to stop him with some help from Dex, who Viddy kidnapped to make the curry sauce.

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.