Mother Brain is the final boss in both the original Metroid and Super Metroid. An early, possible original, model of Aurora Unit, Mother Brain was developed by the Chozo as a supercomputer on their settlement on planet Zebes. Mother Brain regulated scientific data acquired by the Chozo and their experiments, as well as operating Zebes' defense systems and more menial tasks such as regulating water supply and comfort levels in the Chozo settlements.
Even when she was under Chozo control, Mother Brain had a cold and straightforward personality, showing no remorse at killing to protect the Chozo settlement and the Metroid's (who she calls her and the Chozo's 'children') safety. After witnessing the same cold ruthlessness in the Space Pirates following a raid(s) on Zebes and her frustration at the Chozo's weakness in being unable to combat them personally, Mother Brain comes to the conclusion that using these creatures she could bring a true order to the galaxy, after which she 'disposes' of many of the Chozo with their own defenses and assumes command of Zebes.
Mother Brain is also the designer of Samus Aran's Power Suit. In both games, Mother Brain is encased in a glass shell. By firing missiles at the shell, it will eventually break, allowing Samus to attack Mother Brain directly. Various obstacles and hazards, like defense walls and lasers, attack Samus as she tries to defeat Mother Brain. Once she takes enough damage, she will be defeated. In Super Metroid, Mother Brain has a second form, revealing her bulbous head is attached to a mechanical body. She will fire beams of energy at Samus, and drop bombs that will explode in a line along the floor. After pumping many missiles into Mother Brain's head, her weak point, she will begin charging a hyper beam. This is unavoidable and does devastating damage to Samus. After these hyper beam shots bring Samus to less than a single Energy Tank worth of health remaining, she will kneel on the ground, near death. Mother Brain will charge another beam for the killing blow, but the infant Metroid, now fully grown, will attack Mother Brain, draining her life force. Mother Brain survives, however, and begins attacking the Metroid as it regenerates Samus' energy. Once Samus is at full strength, the Metroid rears to attack Mother Brain again, but it has taken too much damage and is destroyed. Samus, who has been super-charged by the infant Metroid, can now fire super-charged beams at Mother Brain's head, and after she takes enough damage she is defeated for good, initializing Tourians self destruct sequence and forcing Samus to make a hasty retreat. Upon her death, Mother Brain's body turns to gray and dissolves.
Mother Brain also appeared as part of a microgame in Warioware Inc: Mega Microgame$! for the Gameboy Advance, where you reenact the Metroid boss fight between Samus and Mother Brain.
An early teaser for Metroid Prime 3: Corruption featured a short video on the existence of Galactic Federation biomechanical computers known as Aurora Units. At the end of this video, a still of what appears to be Mother Brain in her chamber as seen in Super Metroid appears, implying she is an Aurora Unit. In Metroid Prime 3: Corruption, it states that the Galactic Federation designed and commissioned the Aurora Unit Network, although Mother Brain predates the more modern Aurora Units as she was developed by the Chozo. It is possible that the Chozo aided the Galactic Federation in designing their own Aurora Units, meaning Mother Brain would be an early prototype unit.
The Galactic Federation Aurora Units are all linked in a network, and those that acquire viruses, become uncontrollable, or any other such malady will be cut from the network to make sure the malady does not spread. Mother Brain is either isolated from this network after the fall of Zebes, or was never part of it in the first place. Being isolated, or disconnected, from the network could explain her malicious tendencies in the Metroid games.
Mother Brain And The Space Pirates
There is conflicting data on Mother Brain's stance with the Space Pirates. In early instruction manuals (pre Metroid Prime), she is labeled as the leader of the Space Pirates, and controlling them as her subordinates. In the Metroid E-Manga, she assumes control over the Space Pirates on Zebes, making herself, Ridley, and a Chozo named 'Grey Voice' the Space Pirate's commanders. She also offers a young Samus Aran a role, but she refuses to cooperate.
After Metroid Prime, however, the lines are blurred, as the Space Pirate logs and the existence of a separate Space Pirate homeworld indicate a higher power, a group known as the High Command, that are in charge of Space Pirate operations, of which Mother Brain may or may not be a part. It is possible that Mother Brain, like Ridley, are higher powers in the Space Pirate ranks, but not specifically in the High Command. It is also possible that the pirates on Zebes were using Mother Brain's madness and delusions to hide under Zebes' defenses and conduct their experiments on Metroids and the other fauna of Zebes without interference. Her matriarchal stance on the Metroids themselves probably also lead to the Space Pirate capture of the last Metroid in the events of Super Metroid, although the Space Pirates themselves may have had other plans for the hatchling.
Mother Brain was cast as the primary villain of the American cartoon series Captain N: The Game Master. In the show, she was given the ability to speak and was voiced by Levi Stubbs. She is also the only Metroid-related figure that appears in the cartoon. Her underlings in the show are King Hippo of Mike Tyson's Punch Out!! and the Eggplant Wizard from Kid Icarus.