After another Mother Brain eredication, Samus set off to relieve the fears of humanity. Scientists had discovered an artifact revealing a disturbing precense in a dark cloud at a far edge of deep space. While the scientists were preocupied with aiding Samus and researching the hazards, something they never expected happened within the rubble of Zebes. Micro-organisms from the blood of the Zebesians landed on a nearby planet, Fora. They started to chew up the life there, and recreate their own habitat. A seperate research team was sent to discover the qualities of the creatures, but were ultimately forced to call for help. Samus arrives only to find that it's too late to find anyone alive.

Now, not only does she face a stragely familiar enemy, she faces the unknown of a planet recreated from the blood of Zebes.

After taking a few minutes to explore, Samus recognizes a point of no return. Even the rubble of Zebes was recreated. The space pirate clones have no souls. And she fears that the real space pirates may invade to steal Fora as a base. Samus must find a way to eredicate Fora. But she's unsure if it will fall as conveniently as Zebes did.