Samus Aran has conquered the “X” parasite, proving herself as the Ultimate Warrior. Some time after she destroyed the Metroid breeding program by a rogue cell of the Galactic Federation, the mainline Galactic Federation (which had no culpability in the breeding program) received a mysterious video transmission showing a living “X” parasite on the planet ZDR. After the Federation lost contact with their E.M.M.I. robots on the surface of ZDR, they have hired Samus Aran, the last Metroid, to investigate.