The evil witch from part one (Banjo-Kazooie) has returned in skeleton mode, destroyed the heros' home mountain, and killed two nice characters who were around, in the hopes of recovering her body back. To get to her and her sisters' castle, the heros need to collect a big number of jigsaw pieces left around the Isle of the Hags so the all-mighty Jiggywiggy can open the path for them...