Plot

After stopping the threat on the planet Zebes, Samus Aran is asked to eliminate the entire remaining Metroid population of the planet SR388.

Background: in a future Galaxy, representatives of the Galactic Federation agreed that the planet SR-388 had become a universal threat due to one of its native species, the Metroids. These vicious parasitic predators had the potential for widespread abuse, especially in the evil hands of the vile Space Pirates. Should Metroids ever be used as bioweapons by the Pirates, or even escape, then they would have the potential to spread and wipe out all life. The Federation therefore sent a research ship to SR-388 to make sure the planet was ridden of all Metroids. However, an emergency message from the research base indicated that the research ship had gone missing soon after. The base had already sent a search-and-rescue party, but after the initial contact, all communications had gone lost. A special platoon from the Federation Police was sent to SR-388 to finish the job. A single transmission sent during their landing was received; after that, nothing was heard from them again.

Rumours spread, and the whole Galaxy was struck by fear. Obviously, Metroids were still surviving deep below the surface. Even a single Metroid could spawn an entire colony that could easily wipe out an entire planet's population. An urgent Federation conference was called, and it was quickly agreed: bounty hunter Samus Aran, who had successfully defeated the Space Pirates on her home planet Zebes, and had thereby prevented a Metroid outbreak, had to go to SR-388 and make the Metroids extinct. She travelled to the barren planet, and entered the caves, where she also encountered ancient ruins, suggesting the presence of an old civilization, long since wiped out by the Metroids. Samus quickly learned that the jellyfish-like Metroids she was familiar with were simply immature specimens; the creatures were capable of undergoing rapid mutations in their life cycle, in which they shed their outer skin to form Alpha, Gamma, Zeta, and finally, Omega Metroids successively, which were more lizard-like in appearance, and became stronger and more ferocious with every stage. Samus' arsenal and skills were sufficient to defeat all remaining Metroids on the planet. In the deepest cave, Samus finally discovered the source of the Metroids: a gigantic Metroid Queen, that layed the eggs from which infant Metroids hatched, was the final specimen alive. Or was it? Because, after the Queen was defeated, Samus' suit still indicated one remaining Metroid. She proceeded into the cave and discovered a single remaining Metroid egg. It opened up, and to Samus surprise, the infant Metroid did not attack her; instead, it circled around, emitting shrieks of apparent joy, and followed her like a confused child. The tiny hatchling obviously mistook Samus for its mother! Never having considered that such dangerous creatures were capable of such feelings, Samus could not bear to kill the infant. She left and the infant helped her escape the cave. She took it with her on her ship and left SR-388.