Very little was known of Mother Brain, although it was believed that her origins were deeply connected with the Space Pirates: in-game texts, instruction manuals and players' guides described her as their leader, being the perpetrator of their malicious plans and controlling all operations on Zebes. In particular, she is stated to have come up with the idea of using the highly dangerous Metroids as bioweapons against galactic society. Her location in Tourian and the surrounding security emphasized her role of not only being the top ranking member of the pirates, but also as a vital piece of equipment, as her defeat initiates Tourian's self-destruct sequence.
Her personality was an even greater mystery, with only her immobile and mostly expressionless form giving, intentionally or not, the impression of a very cold disposition. Her behavior in Super Metroid indicated she was highly cunning; anticipating a repeat of her previous encounter with Samus, she lured her into a false sense of victory before emerging with the new mobile body, cornering and overwhelming her foe with massive firepower. Despite these calculated moves however, there was evidence of Mother Brain losing control during spontaneous bursts of emotions when, in a fit of rage, she foiled her own plans by destroying the last living Metroid after the creature saved Samus's life, as well as panic when Samus attacks her in retaliation by trying to use every attack in her disposal in an erratic manner.
It was not until the release of the prequel manga that she would be revealed as a highly advanced, artificial intelligence created long ago by the benevolent Chozo, the same race that eventually raised the orphaned Samus Aran as their own. In fact, Samus spent most of her childhood under the watchful eye of Mother Brain when the latter was still an ally of her creators. Their relationship was filled with tension however: when the A.I met Samus, she used a flying monitor to observe her with such scrutiny that it frightened the young child and the former quickly disregarded her as a weak creature that would die from the harsh environment of Zebes. In Samus's adolescent years, Mother Brain occasionally provided assistance and advice during her physical training, albeit condescendingly and with arrogance. A particular event showed Mother Brain deliberately provoking Samus when the super-computer used Work Robots to incinerate several Iono Feria tamed by the orphan under the pretense that they were still dangerous. The A.I displayed concern as she watched Samus grow both in confidence and power, a sign that the former had an unknown agenda planned ahead.
Years after Samus left Zebes, Mother Brain betrayed the Chozo when the Space Pirates invaded the planet and helped them conquer it. Demonstrating her superiority complex, she spoke of her frustrations with her creators and claimed she had long surpassed them. She also calculated that taking control over the Pirates would allow her to bring order to the universe through violence and war, thus she designated herself as master and subsequently gave the role of Space Pirate commanders to Gray Voice, the only Chozo who shared her vision, and Ridley. Mother Brain tried to persuade Samus into becoming a commander through psychological manipulation, stating to have created her Power Suit and that the Chozo's true intention for raising the orphan was to turn her into a bioweapon. She went as far as claiming to be a "parent" to Samus.
Mother Brain was eventually attacked by Gray Voice when he revealed he was only cooperating to win her trust. During the battle, he called her a "defective" product and speculated that she developed fear, hatred and jealousy of other sentient life, in particular of Samus due to the orphan showing far more promise at successfully protecting the cosmos than the rogue A.I ever would. These statements left Mother Brain shaken to the point of affecting her otherwise calm demeanor; she had trouble making proper sentences and she desperately pleaded for Ridley's help when he arrived to rescue her. As Ridley gained the upper hand and mortally wounded Gray Voice however, Mother Brain was quick to sadistically mock her attacker and quipped that he was "just a bird who can't even fly". Samus escaped Mother Brain's clutches during these events and they would not confront each other again until the former's "Zero Mission" years later.
Although Mother Brain claims that she was following her directive per what the Chozo intended, it is heavily implied that she truly desired to have full control of the universe for its own sake. Furthermore, it comes to light that Mother Brain is in fact using the Space Pirates to further her own goals, referring to them and all other beings in existence as simple beasts. She intends on having her forces fight the Galactic Federation until both organizations become sufficiently crippled, at which point she will "cradle" the survivors to "sleep" and, after resetting the universe to zero, help them reach an intellectual level that she deems worthy of life. Thus, achieving her goal of bringing true order. She also plans on using an "evolved" form of the Metroid species to secure her dominion over all life.
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