Shortly after the events of Metroid: Origins, Samus Aran has tracked the location of the Galactic Federation team which visited the uncharted planet G.F. #8791 to a system where she finds a military base being run by the mysterious Colonel she encountered at the conclusion of Metroid: Other M.
Upon landing, she is ambushed and knocked out; stripped of her various abilities. Her captor claims it was to protect the delicate work being done by the scientists on the planet from the rogue Metroid that had joined Samus in her previous adventure since there was no way to know for certain whether or not it had affected her or posed a threat to them.
Getting free with the aid of an old friend, Samus sets out to recover her abilities and explore the surface; learning the secrets of the planet along with what the military is doing there. On the way, she encounters various obstacles and new foes and allies who assist in the completion of her mission.
