In the year 2003 of the Cosmic calendar, representives from the many different planets in the galaxy established a congress called the Galactic Federation, and an age of prosperity began. A successful exchange of cultures and civilization resulted, and thousands of interstellar spaceships shuttled back and forth between planets. Soon, however, Space Pirates began to attack spaceships, threatening the galactic peace. The galactic Police and Galactic Army struck against this aggression, but the pirates's attacks were powerful, and it was impossible to catch them all in the vast reaches of space. So, the Federal Bureau called together powerful bounty hunters to battle the pirates.

In the year 20X5 of the Cosmic calendar, a terrible incident occurred. The Space Pirates attacked a deep-space research vessel and seized capsules containing samples of an unknown species that had been discovered on planet SR388. The Space Pirates's objective was to acquire this life-form: known simply as metroids, these floating organisms were incredibly dangerous, as they could latch onto any other organism and drain its life-energy. Furthermore, it was possible to replicate Metroids in vast numbers by exposing them to beta rays. The hypothesis that the Metroids were responsible for one of the greatest mysteries in the entire galaxy __ the extinction of planet SR388 __ was generally accepted as fact.

If the Space Pirates were able to breed Metroids and use the creatures as biological weapons, the destruction of all galactic civilization would be near certain. After a desperate search, the federation Police discovered the Space Pirates' base of operations on the fortified Planet zebes. They launched a full assault on the planet, but pirate resistance was strong, and the planet could not be taken. All the while, in a room hidden deep within the center of the pirate fortress, the preparations for multiplying the Metroids were progressing steadily.

As last resort, the Federation Police decided on a risky strategy: to send a lone space hunter to penetrate the pirate base and destroy the mechanical life-form that controlled the fortress and it's defenses __ The Mother Brain. The space hunter chosen for this mission was samus Aran. Considered the greatest of all bounty hunters, Samus had successfully completed numerous missions that others had thought to be impossible. Despite her accomplishments. much of Samus's true identity remained wrapped in mystery.

Alone, Samus Aran successfully landed on the surface of Zebes, which was, in fact, the plancet where Samus was raised as a child. Burying all memories of the planet, Samus agreed to carry out this mission and face the traps of Mother Brain. But the question remained: could Samus Aran truly complete this task and return peace and order to the galaxy?