Mother Brain was an organic Chozo supercomputer that was originally created as an administrator for the facilities and computer systems on Zebes. Some time ago, she had gone rogue and betrayed the Chozo to the Space Pirates, who eradicated their civilization on Zebes and made it their base. Mother Brain was one of the leading members of Space Pirate High Command, along with Ridley and Grey Voice.
Mother Brain, along with being an administrative unit, was once an ambassador of the Chozo that negotiated with Galactic Federation representatives from her home in Tourian, a massive underground facility that served as Mother Brain's command center. After she had turned traitor, Tourian became the headquarters of the Zebesian Space Pirates, where they had started a Metroid breeding program. However, she had come into conflict with Samus Aran on two different occasions. They had first clashed when Samus came to eliminate the Metroids bred by the Space Pirates and Mother Brain under orders from the Galactic Federation. Their second encounter was during Samus's quest to rescue the Infant Metroid from the Zebesian Space Pirates. When she was defeated for the second time, Tourian's self-destruction shortly after caused a chain reaction that ultimately destroyed Zebes.
In her first incarnation, Mother Brain controlled various security monitoring systems throughout Zebes that allowed her to observe Samus's progress. She also controlled Tourian's defense systems, including numerous Rinka projectors and an array of turrets in her control room. Finally, she can trigger a powerful time bomb as a fail-safe when she is killed, in hopes of destroying the enemy along with Tourian.
When she was revived by the Space Pirates in the events of Super Metroid, Mother Brain had retained her ability to access the remaining surveillance systems across Zebes and again controlled Tourian's security system. However, the Pirates had also created a powerful robotic body for Mother Brain to use when basic security measures failed. This body was equipped with various powerful weapons, including a sonic beam, a grenade launcher, eye beams, energy shockwaves and the mighty Hyper Beam.