The series focuses on Lan Hikari and his NetNavi, MegaMan.EXE as they build their friendship while dealing with threats from various NetCrime organizations. Along with Lan are friends Maylu Sakurai, Dex Ogreon, Yai Ayano, Tory Froid, and their respective Navis: Roll, GutsMan, Glide, IceMan. Although the series originally remains fairly close to the games in terms of storyline, it begins to diverge greatly partway into the series. For example, there is no evidence showing that Lan and MegaMan were twin brothers in the anime, unlike in the games where it is revealed near the end of the first Battle Network game.

The Rockman EXE anime first aired on TV Tokyo March 4, 2002. It spawned four sequels, Rockman EXE Axess, Rockman EXE Stream, Rockman EXE Beast, and Rockman EXE Beast+, as well as a feature film within the Stream storyline. Three of these four sequels and the film were never adapted in English. Axess was the only sequel adapted.

Licensed by VIZ Media (formerly ShoPro Entertainment before the two companies merged), the English adaptation (titled MegaMan NT Warrior) originally aired on Kids' WB in the United States and TELETOON in Canada (though both networks have stopped airing the series). Axess aired on TV Tokyo in October 2003, while the English adaptation (titled MegaMan NT Warrior: Axess) aired in January 2005 in the United States and April 2005 in Canada. Stream aired on TV Tokyo in October 2, 2004, Beast on October 1, 2005, and Beast+ on April 8, 2006. Kids' WB dropped MegaMan NT Warrior off the TV block at one point and revived only to complete the final episodes from Axess before dropping it again.

Like many English adaptations of other anime series, MegaMan NT Warrior is edited due to Americanization and the shifting of the target demographic toward a younger audience. Among one of the more notable edits made was the editing out of words such as "fire," "bomb," and "napalm," which were thought to be inappropriate for younger viewers. As a result, the names of FireMan, BombMan, and NapalmMan also changed (while the original names were retained in the English games). Other inconsistencies between the English game and anime resulted from similarities in name to American superheroes. For example, AquaMan's name was changed to SpoutMan in the English anime to avoid confusion with the DC Comics superhero of the same name. In addition, swords are blurred, and scenes of MegaMan pointing his buster at the screen are removed in earlier seasons. Curiously, subsequent airings of certain episodes reveal that some of the original edits were changed back—most notably, the FireTower Battle Chip originally edited as "FlameTower" subsequently reverted back to "FireTower". As with WB's other dubbed series (such as Pokémon and Cardcaptors), some episodes were aired out of order, edited together, or skipped entirely. Viewers elsewhere saw the series in its entirety in the correct order. The first series (EXE) has been released on DVD and a few earlier volumes on VHS, but in an edited format only.

EXE is roughly split into two separate storylines. The first concerns the original WWW (World Three) and Mr. Wily's (Dr. Wily) plan on finding the Ultimate NetNavi, culminating in the N1 Grand Prix, a NetBattling tournament. At its conclusion, the Ultimate NetNavi PharaohMan awakens from his slumber and proceeds to claim the net as his own, deleting MegaMan in the process. PharaohMan would eventually be weakened by the two tournament finalists, ProtoMan and a newly-rebuilt MegaMan, leading to his capture by Wily. The second half of the season has the characters take on Grave (Gospel), a NetMafia syndicate spearheaded by Wily that seeks to create a virus beast with the capability to destroy the net. The last several episodes of EXE would serve as a lead-in to Axess.