After the events of Metroid Prime and Metroid Prime: Hunters (According to the official Metroid Timeline) Samus gets a transmission from Galactic Federation HQ they were in pursuit and damaged a ship of Space Pirates and followed it into the planed Aether. While on the surface they encountered violent dark creatures that are know as Ing. The Federation soldiers were wiped out and Samus gets sent there to investigate. While traveling down into the planet her ship is stuck by a storm and crash lands. Samus ventures through Aether and finds great temple which houses U-Mos the leader of a technologically advanced race of organisms called the Luminoth. They were in a war with the ing and are losing. All of there planetary energy is in a parallel world called Dark Aether which the ing reside. Should they get the last of that energy Aether will be destroyed and the ing would take complete control. Samus takes on the task of returning all the planetary energy to Aether so dark Aether would fall and the ing would be destroyed with it.