After crashing on a strange unexplored planet, Captain Olimar must gather the thirty missing parts of his space ship, before his life support runs out in thirty days and he succumbs to the planet hostile atmosphere. Luckily the Pikmin, a plant/insect life form native to the planet, are there to help him. Olimar must gather and lead the Pikmin in this real time strategy game to collect the missing pieces of his ship while combating the planet's strange and sometimes hostile flora and fauna.

The Pikmin come in three varieties with each a special ability. Red Pikmin are immune to fire while blue Pikmin are able to swim and yellow Pikmin can be thrown far. Aside from the story mode there is a Challenge Mode that is unlocked after all the types of Pikmin are discovered in the story mode. The goal in this mode is to grow as many Pikmin as possible in a single day.