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- For placing second in the N1, Lan wins a trip around the world. He starts in the tropical Jawaiian islands, and his friends follow along for some fun in the sun. However, a ghost ship appears, capturing Maysa and Tory. The kids infiltrate the boat to rescue their friends. (en)
- 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. (en)
- The WWW sends viruses to the robotic fish aquarium, causing the fish to rampage through DenTech City. When the fish attack Maysa and the kids, they make a run for the aquarium to delete the viruses behind this mess. (en)
- Maddy kidnaps a water works factory employee. She then forces his son, Tory Froid, to use NetNavi IceMan to freeze the water works network so she can prepare to pollute DenTech City's water supply. Fortunately, Lan and his friends become involved and put a stop to this mess. (en)
- Lan is teamed up with his hero, Commander Beef, in a battle against BlasterMan and StoneMan. The WWW duo is bent on deleting MegaMan, so StoneMan traps him and SharkMan at a lighthouse network to delete them. Lan and Beef dash to the scene to rescue their NetNavis. (en)
- Mr. Higsby is a rare Battle Chip collector who uses his NetNavi NumberMan to steal chips. He traps Yai and her friends in a classroom, threatening to delete Glide if Yai doesn't hand over her rare chips. Lan and MegaMan, who were locked out of the room, work with Roll to crack passwords and rescue their friends. (en)
- Lan's first battle in the tournament is against Miyu, a psychic girl who predicts he will lose against her. Since her predictions have been accurate in the past, Lan becomes nervous, especially when he witnesses Miyu's NetNavi, SkullMan, and his amazing agility. (en)
- 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. (en)
- ElecMan appears to help ward off MagnetMan. As the VirusBeast prepares its final attack on the internet, MegaMan suddenly appears in a new Bug Style to absorb the VirusBeast and the internet himself. However, through Lan's efforts, the bug is alleviated, and MegaMan returns everything absorbed by the VirusBeast back to normal. (en)
- Tory and Maylu have a battle before the tag-team matches begin. However, Lan believes that the NetNavi duo BlasterMan and StoneMan may be up to no good. Sure enough, they're working with WWW and are independent, meaning they don't require NetOps to function. (en)
- PharaohMan sends a satellite on a crash-course toward DenTech City, and no one seems to be able to stop him, not even ProtoMan. However, at the last moment, MegaMan is revived and assists in the defeat of PharaohMan. Not only that, but by using a new ability called Style Change, MegaMan is able to take down the WWW as well. Is this the last they will see of WWW? (en)
- AyanoTech introduces a new internet racing game for NetNavis, and everyone's invited. The NetAgents, WWW, and even Chaud participate in the race. The CutMan Brothers also reappear in hopes of sabotaging MegaMan's performance. (en)
- Roll is on a rampage, disobeying Maylu and beating MegaMan to a pulp. Higsby reappears before it's too late and informs Maylu that the "Devil" chip will be negated if another chip is inserted. Thus, Roll returns to normal, but she's too damaged to continue in the tournament. (en)
- 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 . (en)
- Lan's last venture of his vacation is to try all kinds of different curry—his favorite food. WWW members Mr. Match, Maddy, Count Zap, and Yahoot reunite to trap Lan during his all-you-can-eat curry buffet, but Lan's own friends make a surprise turn to help take the WWW down. (en)
- Yahoot of the WWW uses his NetNavi, MagicMan, to hypnotize everyone in DenTech City into thinking they're wild animals. Lan and Maylu are unaffected, so they go after MagicMan. Chaud Blaze and ProtoMan also make their first appearance to help stop Yahoot. (en)
- Maddy is bored with running a curry shop alongside her former WWW teammates, so she springs at the opportunity to join Grave when Mr. Gauss recruits her. Mr. Gauss plans to drown the NetAgents and Lan at a costume party, but Maddy feels his means are too malicious, so she uses WackoMan to stop him. (en)
- The rich Yai Ayano comes to Lan's school as a new student. Meanwhile, Maddy of WWW uses her NetNavi WackoMan to cause traffic jams all over DenTech City. When Yai finds herself trapped in traffic and in a desperate situation, she jacks in her own NetNavi, Glide, to solve the problem. (en)
- Sal takes the kids on a camping trip into Okudan Valley. There, she meets a childhood friend Dave. But Dave claims to be a Grave member who plans to use QuickMan to destroy the valley's dam. It turns out to be a bluff but CutMan, another Grave member, appears to finish the job. (en)
- 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. (en)
- The events of episodes 33 and 36 are recapped through the point-of-view of the WWW. This episode elaborates on the deletion of TorchMan to the hands of FreezeMan, and the rebirth of TorchMan in the form of HeatMan thanks to the efforts of the enigmatic man named Famous. (en)
- Back home, Lan is introduced to NetCity, an online city for NetNavis to interact in. Meanwhile, a NetNavi named AirMan traps Yai in her bathroom and fills it with hot steam. MegaMan goes to stop the NetNavi who claims to be a member of Grave, a new net-crime syndicate. (en)
- Tora and NetNavi KingMan are champions of NetChess, and he hears that Lan is a formidable opponent. He tricks Lan into a NetChess battle with MegaMan up as the prize. Maylu and Roll join in to help defeat Tora at his own game, but ShadowMan also appears. (en)
- Maylu's first match is against WWW's Maddy, and the two develop a strong rivalry prior to the match. Meanwhile, Lan's next opponent is Mr. Match, and their rematch finally commences. Maylu is able to win her match against Maddy, and everyone rushes to watch Lan's. (en)
- While in Brand City, Lan sees a purse he'd like to buy for his mother, but it's too expensive. He learns of an underground NetBattle game where he can win the purse, but it's really a trap set up by Ms. Millionaire to capture NetNavis for her own personal museum. (en)
- The final N1 match is between Lan and Chaud. During their battle, an unknown force causes the tournament stadium to sink into the ocean, but Lan and Chaud stay behind to finish their match. ProtoMan is declared victor, but a NetNavi suddenly appears and attacks, causing MegaMan's deletion. (en)
- PharaohMan has been revived, and he begins his plan to take over the world. Meanwhile, Lan struggles with the loss of MegaMan, but there may be hope left. Parts of MegaMan's data is retained in his friends' PETs, and Lan's father returns home to help revive MegaMan. (en)
- 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. (en)
- Everyone takes a break from the tournament, so Yai takes them out to eat a fancy restaurant. Chaud appears and antagonizes the kids, so Lan challenges him to a NetBattle on the streets. However, their activity attracts viruses, and Lan unintentionally taps into the power of a Program Advance during the fight. (en)
- 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. (en)
- Lan's bus breaks down while driving through Kingland, so he visits a nearby mansion. It's actually the home of Count Zap who has been persuaded by his mother, Mama Zap, to get revenge on Lan for destroying the WWW. Count Zap traps Lan in a NetBattle where he's shocked every time MegaMan takes damage. (en)
- 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. (en)
- A strange acid rain and viruses loom over NetCity, destroying it. MegaMan and co. jack-in to fend off the viruses, and they soon discover an underground factory that's the source of the mayhem. But when MegaMan goes to destroy it, he meets ShadowMan, an assassin NetNavi hired to delete him. (en)
- The WWW learns of a rare Battle Chip left behind by Mr. Wily that could revive their syndicate. Hidden on a frozen island, they go to retrieve it, but Lan and co. also appear to try and stop them. Mr. Gauss appears also seeking the chip, and a battle ensues between him and his brother, Count Zap. (en)
- Everyone is confused when Rush appears in the real world and everyone's NetNavis begin transforming into cats. It seems a powerful cat virus has escaped, and if it isn't stopped, everyone's NetNavis will permanently become cats. The episode builds up to a Godzilla-sized battle between Rush and the cat virus. (en)
- While investigating a space station on the moon, Commander Beef is suddenly locked outside with a limited air supply. Lan and his friends learn of their hero's distress, so they send their NetNavis to the moon network to save him. There, MegaMan meets PlanetMan, and a very difficult battle ensues. (en)
- FreezeMan is sent to capture Bass, but HeatMan intervenes to get revenge for the deletion of his former being. Bass instead captures MegaMan and begins reading his memories to learn the truth about his existence; he and the Grave VirusBeast were created from PharaohMan's left-over data. Meanwhile, Protoman has a run-in with the Virus Beast. He ends up getting deleted in an attempt to save a young toddler navi. Also, the true leader of Grave is revealed to be Mr. Wily himself. (en)
- The N1 Grand Prix NetBattle tournament is starting. An error in NumberMan's upgrade causes him to go on a rampage, so Lan and his friends set out to stop him. Tory and IceMan rejoin the cast, and the tournament begins with Dex claiming victory in his first match. (en)
- Lan meets a boy named Whip, unaware that he's really the princess of Brightland, Princess Pride. ShadowMan targets Pride because her NetNavi, KnightMan, has a valuable virus protection program. Lan and MegaMan aid "Whip" in the battle against ShadowMan. (en)
- Count Zap and ElecMan of WWW send electro-magnetic waves through DenTech City causing electronic devices to go hay-wire. Lan and Maylu chase a robotic dog onto a subway train when it steals Ms. Mari's purse, and ElecMan plots to crash their train. (en)
- 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. (en)
- A new air-conditioning penguin toy is introduced during a heat wave, but they're really being distributed by Grave. Soon, the penguins begin to blanket DenTech City under a sheet of ice. Lan manages to jack-in to NetCity and finds that FreezeMan is responsible for this mess. FreezeMan is defeated with the help of another new NetNavi named HeatMan. (en)
- Grave's attack begins when they awaken the Grave VirusBeast, a huge monster that begins absorbing the internet. It strikes in NetCity and threatens to delete MegaMan and ProtoMan, but a mysterious NetNavi named Bass appears to chase the monster off at the last moment. (en)
- Lan Hikari's standard level NetNavi receives an upgrade, transforming him into the powerful MegaMan.EXE. Meanwhile, FireMan—a NetNavi working for the World Three net-crime syndicate—has trapped Maylu in a dangerous oven fire. (en)
- 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. (en)
- Lan and Maylu team up against Mr. Match and Maddy, but the WWW has plans to sabotage the match. Posing as Higsby, Yahoot gives Maylu the "Super Great White Angel" chip. However, once inserted, Roll is infected with dark energy and turns against her partner MegaMan. (en)
- Princess Pride calls for Lan to visit Brightland when KnightMan turns on her. However, he's really under the hypnotic powers of MoltanicMan, a Darkland NetNavi who plans to destroy Brightland's firewall and invade the country. (en)
- Deciding to perfect the Program Advance, Lan begins training before his next match with Yahoot and MagicMan. Miyu also assists him. Lan is able to perform the technique and defeat MagicMan in battle, but soon discovers that Chaud also knows the technique when he uses it to defeat ElecMan. (en)
- Mr. Match infects the stadium network with viruses, causing the entire stadium to heat up like a sauna. Likewise, TorchMan is powered up from the solar energy. Yai, Dex, and Tory set off to delete the viruses before Lan collapses from the heat. (en)
- The match begins. Chaud insists on working alone, so he takes on BlasterMan and StoneMan single-handedly. BlasterMan is deleted, but StoneMan has a regenerative core that makes him difficult to delete. However, ProtoMan becomes overcome when Chaud realizes he lost the chips needed for the Program Advance in the elevator shaft with Yai. (en)
- The girls enter a contest to be just like Aki, a virtual pop singer. However, contestants go missing, so the boys dress as Aki to investigate the situation. A virus has infected Aki causing the mayhem, so MegaMan, GutsMan, and Iceman jack-in to rescue their idol. (en)
- Mr. Match demands a rematch with Lan, so TorchMan sets out to find MegaMan. Instead, he finds Roll, who is currently arguing with MegaMan . To prove her worth to MegaMan, Roll takes the invitation instead, and meets up with TorchMan for battle. (en)
- Mysteriously, Higsby has become very wealthy, and Yai's family has gone broke. Mr. Gauss is responsible, a member of Grave who is using MagnetMan to switch people's bank accounts around. Lan and Chaud investigate the situation, but Gauss escapes. (en)
- 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. (en)
- Yai's father, the president of AyanoTech, promises to let her and her friends play the new video game the second it releases at midnight. While the kids patiently stay awake to play it, Count Zap plans to steal the game data using ElecMan. (en)
- Lan and Chaud are teamed up for their next match against BlasterMan and StoneMan. Before the battle, Chaud is leaving a restaurant and Yai decides to follow him. However, the two become trapped together in an elevator. They have to overcome their differences in order to escape in time. (en)
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