Gruntilda is back, and only Banjo and Kazooie can stop her master plan! Travel through time encountering puzzles, battles, and meeting friends old and new in this all-new Banjo-Kazooie adventure!

Two months have passed since Gruntilda fell from her tower, putting the events of the game before those of Banjo-Tooie in the timeline, and she is still trapped beneath the boulder. After trying to push the boulder off of herself, her loyal henchman Klungo decides that a different plan of action is required, so he builds a Gruntilda-shaped robot, the Mecha-Grunty, into which Gruntilda's spirit transfers. While her real body would still be stuck underground, she could now initiate a scheme of revenge against Banjo and Kazooie at will. Kidnapping Kazooie, she goes back in time (supposedly 20 years, although the actual amount of time is unknown) with the plan to prevent the bear and bird duo from ever meeting in order to erase her prior defeat from history and restoring her to her previous self.