Mother Brain lies in the central base of the fortress planet Zebes, the home of the space pirates. Its aim is to cultivate the Metroid to multiply and conquer space. The entirity of her energy comes from Zeebetites. For all intents and purposes, she commands all that is on Zebes, or failing that, anything that will obey her. She generally dislikes being blasted by missiles, but hell... who wouldn't? Rumour has it that she herself raised both Kraid and Ridley.

Mother Brain has been the figurehead of all minions in the enemy-union. In short, virtually all enemies, save a few exceptions, obey her every command. Last seen, she had found her way back to the mortal coils of life thanks to a failsafe method should her first body be destroyed. She is now... a clone of herself. Her latest creation, the mechanical Samus, was created from a piece of material brought back from ZR388, and failed spectacularily. However, it has become apparent that she has teamed up with Geruta... again... but this time the duo has accomplished killing Ridley. Unfortunately, he got better. Lately, she has been attempting to shake Crocomire Hunter off of her, whom has wrangled her but good.