At the outset of the first episode, the hero of the series, Kevin Keene, a teenager from Northridge, California, and his dog, Duke, are summoned to another universe known as Videoland by being sucked into a vortex that formed in his television, called the Ultimate Warp Zone. In order to fulfill an ancient prophecy, Kevin is destined to become the hero "Captain N: The Game Master" and save Videoland from evil forces, which are led by Mother Brain from the floating world/fortress called Metroid. By the time Kevin arrives on the scene, Mother Brain has almost succeeded in capturing the Palace of Power and conquering all Videoland. Kevin (who in Videoland is armed with a Zapper and a belt buckle shaped like a NES controller) and Duke appear suddenly on the other side of the Ultimate Warp Zone before the N Team, which consists of Princess Lana (the acting ruler of Videoland; a later episode explains the absence of her father the King), Simon Belmont, Mega Man, and Pit (Kid Icarus), none of whom show any confidence in Kevin's ability in the beginning. After Lana is kidnapped by the enemy shortly after Kevin's arrival, the reluctant group puts their differences aside to go on a rescue mission where Kevin eventually gains the others' confidence.

In most episodes, the N Team's enemy is a group of video game villains usually led by the boisterous and loud Mother Brain who is accompanied by her minions: the sheepish Eggplant Wizard, the thuggish King Hippo, and the scheming Dr. Wily. A 'villain of the week' is featured in some episodes when a particular video game becomes the setting (such as Malkil of Wizards and Warriors). Donkey Kong also makes an appearance as a territorial, belligerent, Godzilla-sized gorilla in some episodes, but usually serves as a dangerous neutral character posing a hazard to friend and foe alike.

Further recurring characters make an appearance as either friend and foe. The Count (Castlevania) makes multiple appearances, along with Dr. Wright, Link and Princess Zelda, and, from season two onward, Game Boy joins the N Team.

The focus of the show is mostly action-adventure sourced from the video games they parody, with comedic relief forming in the characters' interactions with one another and the environment. Sometimes, humor also stems from the comparatively loose interpretations of the laws of reality that apply in Videoland.

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