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She begins perceiving all life forms in the Bottle Ship not under her control, including the scientists, as a threat and controls the Desbrachians to attack in order for her to take over. She begins calling herself Madeline Bergman, the name of her former human friend, and tries to manipulate Samus into believing she is an ally.
It is unknown if her actions influenced Ridley at all, who had been reborn in a new cloned body. It is possible she may have been able to direct him upon his body being drained and his still-existing molecules being sucked into the Metroid Queen (which was destroyed by Samus, meaning his molecules would return to his drained body).
Regardless, she is destroyed soon after the Queen, being anticlimactically shot down by the Federation soldiers as soon as Samus takes care of the Desbrachians, thus destroying what may have been another Mother Brain.
Ridley, however, was to be resurrected yet again in Metroid: Fusion.
It is possible that MB was under the manipulation of Phantoon, who shows up as the true final boss post-credits.
Metroid Prime 3: Corruption