In part one, Max Powers delivers a crate full of microchips to Nintendo of America and talks with worker Brett Randalls as he plays Metroid. Tara, one of Brett's coworkers who he has a major crush on, accidentally spills her coffee on the crate causing it to explode. Brett is peppered with the chips, which also infiltrate a game pak and give birth to the artificial intelligence EMERALD, who explains that the explosion has given Brett special powers, like the ability to shoot electrical bolts, control the light spectrum, and temporarily materialize characters and items from inside video games. Unfortunately, the explosion also brought Mother Brain to life from inside Brett's game. Brett and Tara find Max, who'd left to find a broom to clean up the mess, knocked out by Ganon.
In part two, Brett battles Ganon and uses his powers to reveal Ganon when he turns invisible. However, when the fight is interrupted by Morgana, the receptionist with a crush on Brett, Ganon and Mother Brain disappear. Brett goes to get help in defeating them and makes Link appear from The Legend of Zelda. Link and Brett (as Captain Nintendo) battle Ganon, and Brett finishes him off by stabbing him with a silver letter opener. Because Mother Brain was using her own energy to control Ganon, she fades away as he does. EMERALD warns that Mother Brain isn't really dead, only in hibernation, and will return once she's recovered her energy. With this ordeal under his belt, Brett finds the courage to ask Tara out, but she declines because she doesn't date guys she works with.
To finish the story, Brett vows "If you can hear me, Mother Brain, listen well: You will not succeed. For wherever this is an injustice to be rectified, a person in need of rescue, or a quest to be taken up, there also will you find the power of Nintendo...and it will always triumph. I promise."
A running gag throughout the story is the people Brett meets talking about modifications they'd make to his costume. Even Link makes one before disappearing back into the game.