It is galactic year 20WX, several years before the events in the original Metroid. Hydra, a veteran smuggler, is engaged in what she expects to be a “routine” delivery mission to the planet Zebeth. But a nearby patrol of Federation fighers suddenly decloaks and opens fire on her vessel, damaging its engines. Unable to escape pursuit, she instead decides to attempt a crash landing.

Once the surface, Hydra has no means to hide her downed vessel, and realizes she must think fast. A quick scan of the area reveals a nearby teleportation device. Where could it lead? With no other options, she discards her ship with all of its cargo and enters the teleporter. The game begins with Hydra reappearing inside the labrynthine tunnels of Zebeth.