The game's story revolves around Craft Island, a peaceful island for the Yoshis. One day, Kamek turns all but two of the Yoshis into Wonder Wools as a favor to Baby Bowser, who wishes to use the accumulated yarn to construct a new castle in his name. When the remaining two Yoshis notice Kamek inadvertently dropping Wonder Wools around the areas next to Craft Island, they set out on a quest to collect them all and thus restore all of the unwoven Yoshis.
After Baby Bowser is defeated at his castle, Kamek uses his remaining Wonder Wools to make him more powerful. Despite this, Baby Bowser is defeated again, returning all of the remaining unwoven Yoshis back to normal. The Yoshis return to Craft Island, while Baby Bowser takes some time to "think about what he's done".
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