An episode in the Metroid Prime series which started on the GameCube, this game takes place between Metroid Prime and Metroid Prime 2: Echoes. Interstellar bounty hunter Samus Aran is sent to the distant Alimbic Cluster by the Galactic Federation to investigate a message saying that the source of ultimate power lies in this desolate part of the galaxy, once home to an advanced culture.

Samus is not alone, however. Other races have heard this mysterious message, too. Six other bounty hunters, each with unique characteristics, will do everything to get their hands on the Alimbic relics for their own reasons.