Samus is dispatched by the galactic federation to infiltrate the centre of the sinister Space Pirates fortress on planet Zebes, exterminate all Metroid organisms and destroy the Pirates' leader, Mother Brain.
After discovering a possible pirate colony on Tallon IV, Samus has again prepared for war hoping to end the pirate threat forever. Though, the space pirates plans are more sinister than imaginable.
After losing contact with a squadron of elite soldiers on SR388, the Galactic Federation are positive that a Metroid presence is still surviving on the planet. Samus has been tasked to exterminate the Metroids once and for all.
Unable to bring herself to exterminate the infant Metroid, Samus has taken it with her and is now personally delivering it to the Galactic research station at Ceres so that scientists can study its energy producing qualities.
