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Toots is seen in Gobi's Valley, Toots is in one of the pyrimids, he is in the pyrimid with the Kazooie target above it, to enter you must bash the target and then you may enter. Inside is a character named Rubee and Toots is at his side. There is a basket in the middle of the room and another basket in the room going round the first basket, if you put enough eggs into it Rubee will play his instrument and Histup will appear and help Banjo and Kazooie gain the Jiggy. Toots will dance along to the music Rubee plays.
In Banjo-Tooie the pair meet Toots again, he is now King Jingalings pet and resides on his throne. When Grunty orderes an attack on King Jingaling to suck his lifeforce, Toots is also caught and he is disintergrated, all thats left are his blinking eyes. Later on when Banjo restores King Jingaling to his rightfull state, Toots is also seemingly restored and goes back and sits on the throne with King Jingaling.
There seems to be some debate whether Toots is the same Toots in Banjo-Kazooie and Banjo-Tooie, or if they are diffrent creatures. Rare has not commented, but has gone out of there way to give them both the same name, so it is more likely there the same character.