The trilogy closes as corruption creeps over the universe… and into Samus Aran. Using the Wii Remote and Nunchuk, players control Samus as she partners with other bounty hunters, shoots down enemies, and explores alien worlds in a harrowing mission to stop the mutagenic Phazon from spreading across the galaxy.

The Galactic Federation's Base Sector Zero is under attack by Space Pirates. Samus must boot up the generator to restore the defense systems. But at the end of her path, someone awful is waiting for her. The war initiated by Dark Samus and the Space Pirates rages across many planets as they attempt to corrupt each with Phazon seeds. Players use the Wii Remote and Nunchuk to explore alien landscapes, hunt for weapons and information, and destroy the seeds. Saving the planets from Corruption isn't enough, though. Eventually, players must take down Samus' mortal enemy, Dark Samus. Besides using the Wii Remote and Nunchuk controllers to pull off amazing feats like aiming and blasting in midair or at a full run, players also will have an array of different weapons at their disposal.