The robotic entity know as Matrix-Prime is really an artificial construct used by Brains, the leader of the Gang, enemies of the Pre-Crisis Supergirl. Supplied by the mysterious Council, Brains used the robot as her new form to attack again Supergirl, but in the heat of the battle the feedback make the mind of Brains be fused with the robot, making than the robot was indeed inhabitated by Brains' mind.
Post -Crisis was stablished than many of the Supergirl pre-Crisis adventures were starred by Power girl instead.
Later, Matrix-Prime was seen leading the Gang as a dealer from the underground specialized in traffic with exotic weapons. When the fall in disgrace Will MacIntyre appeared in his hideout to sell some Justice League memorabilia, Matrix-Prime mocked him and threatened with kill him. Scared, MacIntyre summoned the djinn LKZ, who killed the whole Gang in a blink and most probably erasing the mind of Brains from the robot.
Brains, the human handler of Matrix-Prime, reappered later against Supergirl, leading a new Gang. If she was the original Brain who survived the LKZ attack, a look-a-like or a rebooted version, is unknown.