The Space Pirates, merciless agents of the evil Mother Brain, have stolen the last Metroid from a research station, and once again Mother Brain threatens the safety of the galaxy! Samus Aran must don her awesome array of high-tech weaponry to retrieve the deadly Metroid hidden deep within the cave-riddled planet Zebes. Super Metroid features excellent graphics, with a huge variety of enemies and worlds to explore. The side-view action will be familiar to many players, only now there are new weapons and items, including the Grappling Beam, which allows Samus to swing across large chasms, and the X-Ray Scope, which reveals secret passages.

After Samus completed her mission and eradicated the entire Metroid population on SR388 as commanded by the Galactic Federation (sans the Metroid Hatchling, which she nicknamed "Baby"), she brought the Hatchling to the Ceres Space Colony for research. However, shortly after she left, she received a distress signal from the Station and returned to investigate.

When Samus arrives at the Space Science Academy where the Baby was being studied, she finds all the scientists slaughtered and the containment unit that held the Baby missing. Upon further exploration of the Station, she finds the Baby in a small capsule. As she approaches, Ridley appears and grabs the capsule. After a brief battle, Samus repels Ridley, and he activates a self-destruct sequence to destroy Ceres.

After escaping the explosion, Ridley flees to Zebes, and Samus goes after him.