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The most anticipated move of Banjo-Tooie, the Split-up ability can be learned in the game's third world, Witchyworld, just behind the Big-Top Tent. When you find a pair of Split-up Pads, have Banjo step on the Banjo pad and press A button (N64), and Kazooie will leap out of her backpack onto the Kazooie pad, putting the player in control of the bear. In order to switch to Kazooie, stand on the Banjo pad again and press A button (N64), and do the same with Kazooie on the Kazooie pad to switch back. Certain spots will also have colorful sparkles, called Swap Gas, which will allow the player to switch between characters by pressing A button (N64) while standing in them. To rejoin the pair at any time, simply have one run into the other. You cannot leave a world (or an Isle o' Hags area) while the bear and bird are still split up.

An obvious advantage of splitting up is that both characters can now learn their own set of moves to fit a greater variety of situations. Also, each character has their own attributes. Banjo alone can still swim underwater, hang on edges, and climb objects, while he only learns one attack but multiple "utility" moves. Kazooie retains her ability to fire Eggs, fly, Shock Jump Spring, and use footwear, as well as learns new offensive moves. Lacking Banjo's weight also improves her agility and performance. At maximum energy, Banjo carries eight honeycombs and Kazooie has seven. At minimum, Banjo has three honeycombs and Kazooie has two.

Certain switches encountered in later worlds can only be activated when a certain character stands on them. Such switches often come in pairs which must be activated simultaneously, and are accompanied by Swap Clouds so the player can switch between characters. However these and all other Swap Clouds are only visible when the duo is split.

Jamjars' Rhyme

Separate skills
are what you lack,
so let's get Kazooie
out of your pack!
Find your pads
is what you do,
pressing A button (N64)
makes one become two!

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