The Story take place after Pikmin 2. When Olimar, Louie and the President goes back to Hocotate, some plasm from the Waterwraith falls off of Olimar and Louie's suits. Solarwind carries it all back to the Planet of the Pikmin. It brings the plasm to a forest area with many life, the plasm mutates due to the pressure and makes the Shadowraith! It bites all of the creatures there to get some DNA from them, this lets it take the bits of DNA it got to transform it into a shadow DNA. This makes him make a shadow clone of the creature who owns the DNA. The Shadowraith spent 3 years making Shadow Enemies on the Pikmin Planet.