The Federation was in ruins. It all started with a meeting on Earth: Space Pirates had stolen three Aurora Units from the Federation. Samus and a new bounty hunter, Hunter, had been sent out to find the Aurora Units. Before they even started their mission, the Space Pirates had attacked Earth, with five Leviathan Seeds, and their entire armada. In a desperate attempt to stop them, Admiral Dane crashed the G.F.S Olympus into the Pirate's Mothership, only managing to weaken it. Unfortunately, Samus had been in the middle of the collision, stuck inside a dogfight, and had barely made it out alive. The last thing she remembered seeing before she blacked out was Hunter's rusty ship heading straight for her...