Samus Aran goes to a planet called SR388 when the Galactic Federation told her to exterminate the Metroids that live on it . After exploring the underground areas of the planet and killing almost every Metroid , she fights and kills the Metroid Queen . The story of Metroid II follows the protagonist and playable character Samus Aran , who is sent on a mission to exterminate the Metroid creatures from their home planet SR388 before the antagonistic Space Pirates obtain and use them .