Mother Brain is the leader of the Space Pirates, past ally of the Chozo and Samus Aran, and now her enemy. She is a malicious intelligence capable of using telekinetic waves to control even Metroids. It is assumed that the Galactic Federation's Aurora Units were based on her.
Mother Brain was created years before Samus was born by the Chozo so that they could pile their combined intelligence into her, which she would then use to craft a way to stop the X-parasites. She successfully created the first Metroid, depositing them on SR388 and stopping the parasites. She was then used for maintaining Zebes. Years later, when Samus arrived, she helped oversee her training, as well as creating the Power Suit. Later still, she began to see the worthlessness of the Chozo, stating to Samus that beyond her existence there is no value in having the existence of the Chozo, wishing to 'discard them'. As such she forged an alliance with the Space Pirates, seeking to direct to restore order to the cosmos by ruling it. She also sought to have Samus on her side as a commander, as with her they'd be no stopping the Space Pirates. To this end she played with Samus' mind, telling her that she is her Mother, and that Old Bird only brought her to Zebes to convert her into a bioweapon. Samus still revolted however and escaped Zebes.
Mother Brain has the ability to use telekinetic waves to control organisms, and is also capable of firing beams from her eye, at least in Metroid: Zero Mission and Super Metroid. In Super Metroid she also displays the ability to be able to 'evolve', leaving her tank and becoming an enormous Tyrannosaurus Rex-like monster.
Mother Brain, as evidenced in the manga, seems to praise herself as a higher species to everyone else, discarding the Chozo as unnecessary and ruling the Space Pirates in a heart beat. Her overall plan is to set the universe to zero and become its ruler by having the Galactic Federation crippled by her Space Pirates. She also mocks Samus at several points and purposefully tries to infuriate her by having Work Robots kill off many Iona Faria.
Mother Brain has appeared four times in the series so far.
Metroid was the first game in which Mother Brain appeared. Samus was dispatched to Zebes with the sole purpose of destroying her and the Metroids, and could only reach her by destroying both Ridley and Kraid to enter her home of Tourian. She was the final boss of the game, and was guarded by various turrets and Rinkas. Defeating her required Samus to smash her stasis tank and then finish her with Missiles. Her defeat sets off a self-destruct sequence, which destroys the Space Pirate's base. This would have been her, Ridley and Kraid's end had orbiting ships such as the Frigate Orpheon not salvaged their remains and revived them.
 Super Metroid
A revived version of Mother Brain appeared in this game as the final boss, restored by the Space Pirates. Samus yet again had to fight her commander's to enter Tourian to face her. She is fought the same way as in the original Metroid, however upon defeat she strips the machinery and casing, becoming a huge monster. Samus is defeated by Mother, though is luckily saved by the Baby Metroid, who then dies in turn. It thankfully restored Samus' energy and weaponry,a dn allowing her to use the Hyper Beam to destroy Mother Brain.
 Metroid: Zero Mission
Being a remake of Metroid, Metroid: Zero Mission was another game that Mother Brain appeared in at the end of this game, and was guarded and could be killed in a similar manner, but with one key difference: once the glass was broken, Mother Brain would fire charged shots from her eye, which is the weak point. Only when the eye is open is she vulnerable to damage from Missiles, Super Missiles, or the Charge Beam. Again, she causes the self-destruct to destroy the Pirate base.
 Metroid: Other M
The most recent game in the Metroid Series is also the last game in which Mother Brain had appeared. She was only in Samus' flashbacks, and she looked more-or-less the way she did in Super Metroid. However, the Galactic Federation created an Artificial Intelligence program was designed that could control an army of cybernetic Zebesians and Metroids, based upon Mother Brain. The AI, through interaction with Metroids, eventually formed a soul and took on the form of a living person, who was called MB, or Melissa Bergman. Unfortunately for the Federation, Mother Brain's malicious thoughts bled through and she began asserting herself over others and contradicting their viewpoints, becoming sure in only herself. The scientists on board the Bottle Ship decided to have her reprogrammed to not have a soul so she would be easier to handle, however the presence of the woman she deemed her 'mother', Madeline Bergman, caused her to snap. She turned hostile, the evil tendencies of Mother brain finally asserting themselves. She controlled the Zebesians and other lifeforms to brutally slaughter everyone aboard, before hatching a plan to intercept the Galactic Federation Headquarters and unleash hell upon civilization. She was however stopped by the combined efforts of Samus Aran and Anthony Higgs, and executed by the Federation Armada.
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