After exterminating the Metroids on SR388 in Metroid II: Return of Samus, Samus Aran brings the infant Metroid to the Ceres Space Colony, likely staying at the colony while scientists study the young metroid. The scientists' findings show that the powers of Metroids could be harnessed for the benefit of mankind. Leaving the Metroid in their care, Samus leaves Ceres in search of a new bounty to hunt. However, shortly after leaving, Samus picks up a distress call from Ceres and returns to investigate. As Samus explores the space colony, she finds the power is out and eventually finds bodies lying about the room that contained the Metroid. She continues investigating and meets Ridley once again — holding the container with the Metroid inside in his claws. Samus and Ridley fight, though Ridley flies out of the station. At the same time, a countdown begins, showing Samus has 60 seconds before the station explodes. Samus quickly returns to her gunship and flies to the nearby Zebes in pursuit of Ridley.
The Space Pirate base that was destroyed in the first Metroid game has now been rebuilt. It should be noted that a whole section of Crateria, the first section of Zebes, looks like Tourian from the Metroid (dubbed Old Tourian), with Mother Brain's old control chamber inferring that it is the remains of the Space Pirate base from the original Metroid. Samus sets out to locate the infant Metroid and prevent the Space Pirates from gaining use of its powers. As in the previous games, Samus is forced to delve into the planet through its many caverns to hunt down the Space Pirates. This time, however, Samus can only enter Tourian by destroying four bosses: Kraid, the giant lizard whose base makes up a large part of Brinstar; Phantoon, an entity that controls the destroyed Wrecked Ship and reroutes its power supply to Mother Brain; Draygon, a crustacean monster that occupies a submerged pirate lab in Maridia; and Ridley himself, who controls Norfair and his lair.
After defeating all four of the bosses, and finding Mochtroids, unsuccessful clones of Metroids, Samus battles her way through Tourian, encountering newly bred Metroids. After passing through several corridors filled with Metroids, she encounters a Metroid larger than the rest. Before she attacks it, the giant Metroid drains 99.9% of her life force. However, it seems to recognize Samus; it appears that this huge Metroid is the infant taken from SR388. According to the Nintendo Power Player's Guide, the huge Metroid is named "Super Metroid".
After the Metroid departs, Samus recovers her energy and confronts Mother Brain. After Samus destroys the creature's stasis tank and inflicts enough damage, Mother Brain attaches itself to a giant mechanical body and the battle begins again. During the battle, Mother Brain uses a massive burst of energy from its eye, nearly destroying Samus. Samus finds herself unable to move while Mother Brain charges up to finish her off. Before the final blow can be inflicted, however, the once Infant Metroid suddenly attacks Mother Brain, draining its energy until it appears dead. The Metroid then attaches itself to Samus and begins feeding its energy to her. However, Mother Brain soon recovers and begins firing upon the hatchling, weakening it until it lifts off of Samus. A final shot destroys the hatchling, leaving its remains to fall upon Samus.
Pulsating with energy from Mother Brain, Samus now possesses the almighty Hyper Beam. With it, she easily destroys Mother Brain, who falls to the floor and turns to dust. This in turn triggers a self-destruct sequence, giving Samus three minutes to escape through the emergency evacuation shaft of the original base. Along the way, Samus rescues several Etecoons and a Dachora and makes it to her gunship just in time and takes off, watching the planet explode in a flash of light.