Mario and Peach get a letter from Prism Island, which they find out is a color-drained Toad. This causes Mario, Peach and another Toad to set sail for Prism Island.
When they arrive there, they see the island is drained of its color. Then they find a new partner, whose name is Huey. So it's up to Mario and Huey to go on an adventure to restore the color to Prism Island.