Mother Brain is an AI built to oversee the function of the Geno Dome, and responsible for the creation of Robo and Atropos XR. After Lavos erupted in 1999 A.D., Mother Brain became corrupted and reasoned that since the planet would eventually recover, a new nation of robots should be established to inherit it. To this end, Mother Brain also tried to convince Robo that his function was to kill humans; Atropos was also brainwashed in this manner, but Robo defeated them both. Subsequently, all computer systems in the Geno Dome went offline.
Mother Brain's ultimate mission was mangled in the English translation of the game, which suggested that Mother Brain was attempting to stop Lavos from sending its seed out to other planets and causing further destruction. This is not true; in the Japanese, Mother Brain stated that the planet would eventually recover, and made no mention of stopping the Lavos spawns.
Mother Brain served as a template computer system for FATE, and it is speculated in game that FATE will wanted to create its own species. Ultimania also states that Lucca is the one who developed the Mother Brain AI, but this conflicts with Trigger, as if Lucca developed the AI after returning from Chrono Trigger, then her departure from the present era should mean that Mother Brain would not exist for the party to see in the future (a case of the Guardia Line Paradox).