Facing against Mother Brain after it destroyed the fully grown baby Metroid, Samus had destroyed the AI. However, sounds of crying came from the mound of the dead Baby Metroid to find a young humanoid... You. Fleeing her old home planet of Zebes after freeing the Etecoons and Dachora from a secret room right before it blew up due to self-destruct, she has decided to take you in as her own child.

It had been over a year since then and you and the animals had been living with your mother on her secret compound. Samus had run dry with jobs, so she was taking this opportunity to relax and readjust before something new came up.

Oh, my little miracle... What would you like for dinner tonight? I don't have anything planned.