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|“||Banjo-Tooie, simply put, is incredibly unimaginable.||„|
|~ Fran Mirabella III, IGN|
Following the previous events of Banjo-Kazooie, Gruntilda has been stuck underneath a rock for 10 years and has finally been freed, although she is a skeleton of her former self. Her, along with her two other sisters, create a "drill" that can destroy anything in it's path, so they aim for Banjo's house. Inside Banjo's house, Banjo, Kazooie, Bottles, and Mumbo Jumbo are playing cards, but they hear the commotion, so Banjo, Kazooie, and Mumbo leave the house leaving Bottles inside, waiting to finish the game. Gruntilda destroys Banjo's house, and the burnt Bottles stumbles out of the building and dies, his ghost hovers above his body for the rest of the game. After leaving his house, Gruntilda's faithful but dumb lackey Klungo can be seen standing near an open cave, beckoning for them to follow. After proceeding into the cave, Klungo reveals a potion to help him fight the duo, however, he ultimate fails and runs off.
Banjo and Kazooie seek out help from King Jingaling, who has a problem of his own, and reward them with their first jigsaw piece as incentive to help him. After Banjo and Kazooie leave, a cutscene shows Gruntilda and her sisters standing around a monstrous device, called the B.O.B. which will help Gruntilda get her "skin back" by draining the life out of flora and fauna. Banjo and Kazooie only have a short amount of time before the entire world becomes a lifeless zombie.
Gameplay is very similar to Banjo-Kazooie, with the addition of new collectibles, new levels, and new learnable moves.