Samus Aran is sent back to planet SR388 to assist a Biologic Space Labs investigation team. While on the planet's surface, Samus is infected by a previously unknown parasite, known as X. The X parasite nearly kills Samus, but fortunately she is saved by a vaccine made from the Metroid she saved on Zebes. Shortly thereafter, an explosion rocks the Biologic Space Labs. Now Samus must investigate the Space Labs, which are orbiting SR388.