The game takes place following the conclusion of Banjo-Tooie, in which Gruntilda's body is destroyed by Banjo and Kazooie. Eight years have passed since Gruntilda's defeat. While Banjo and Kazooie are eating pizza, playing video games and listening to the radio, they discover Gruntilda's detached head returning to Spiral Mountain. They are about to fight when they are stopped by Lord of Games (L.O.G.). He attempts to settle the conflict between the two by devising a series of worlds and challenges. He uses his powers to give Gruntilda an artificial body and to restore the duo's physical fitness, but not their moves from previous games.