The Story begins with Sonic and his friends being lost after finish up on their last mission from Lady Tsunade and they find valley that has a spiraling mountian. Then it cuts to a foul-tempered witch named Gruntilda learns from her cauldron that she is not the most beautiful girl of all, but instead a bear named Tooty, who is Banjo's sister. In retaliation, Gruntilda creates a machine which can transfer a person's level of beauty to another, with which she intends to use with Tooty She then abducts Tooty from Banjo's house while he is sleeping. In response to the kidnapping, Kazooie wakes Banjo up and the two set out to rescue her.
Banjo and Kazooie learn from their friend, Bottles the mole, that Tooty was captured by Gruntilda and suggests they need some training to collect musical notes and jigsaw pieces to progress through Gruntilda's lair. By the time most of the musical notes and jigsaw pieces are gathered, our heroes face Gruntilda in a trivia game show named "Grunty's Furnace Fun". The game presents questions and challenges related to certain aspects of the game. After going through several game boards, our heroes win the game and Gruntilda flees. Reunited with Tooty, Banjo and Kazooie return home and celebrate with their friends with a barbecue. However, Tooty reminds everyone that Gruntilda has fled and tells Banjo and Kazooie to defeat her.
The pair return to Gruntilda's lair and use her cauldron to get to the top of the tower, where they confront the witch. Gruntilda attacks Banjo and Kazooie with her broom and energy blasts, but they summon five giant Jinjos, some friendly creatures, and destroy Gruntilda's broom. Banjo and Kazooie then use another giant Jinjo robot called the Jinjonator to send Gruntilda falling to her demise. Returning to their home, Banjo and Kazooie visit a beach with their friends and celebrate their victory. The story ends with Gruntilda swearing revenge against Banjo and Kazooie and also Team Sonic while her henchman Klungo tries to move the boulder covering her.
- These is a teaser trailer made for Youtube featuring the intro of Banjo-Kazooie done by BrentalFloss and the members of Team Sonic dancing along with song.
- This is the first movie to Feature Meowth after the events of Sonic the Hedgehog and The Phantom of Illusions
- Guest Staring: Wendy and Charlie