Metroid Fusion is a side-scrolling action game that's more in line with the series' NES origin than its GameCube contemporary, the first-person action game Metroid Prime. In this one, players take the bounty hunter Samus on an extermination mission through a research facility to kill X parasites--nasty creatures that absorb and assimilate the powers of their host. After she survived an X attack through the use of a vaccine made with X parasite DNA, she can now absorb the parasites to regain health and obtain special powers, like the morph ball, space jump, and wave beam. The problem is that the parasites are quickly making their way through the research lab's many dangerous projects and subsuming their abilities.

As a special bonus to GameCube owners, Metroid Prime and Metroid Fusion can each unlock special features in the other game via the Nintendo GameCube Game Boy Advance cable. For example, by completing Metroid Fusion, you can unlock the original NES version of Metroid in Metroid Prime. By completing Metroid Prime, you can unlock Samus's fusion suit for use in Metroid Prime.