Two years have passed since Gruntilda the witch was defeated by Banjo and Kazooie. She is revived by her two sisters.

In the aftermath of Grunty's return, Banjo and Kazooie search for their friends.

Banjo and Kazooie pursue Grunty's tracks and are confronted by one of her most loyal servants.

Grunty puts her evil plan in motion, whilst Banjo and Kazooie are left to deal with the aftermath.

Banjo lacks the courage to inform Mrs. B about Bottles' unfortunate fate at the hands of Grunty, while Kazooie is eager to deliver the news.

Banjo and Jamjars embark on a quest to find Kazooie, while Kazooie discovers a secretive ancient society hidden within the depths of the wooded hollows.

Banjo must secure passage on the Chuffy train to Cauldron Keep in order to thwart Gruntilda and find Kazooie.