Brian the Brain was a super computer used by V.E.N.O.M..
Brian was a top secret computer with limited thinking and reading abilities developed at the Bolt Research Corporation to control their modified nuclear submarine, taking the place of captain and crew. BRC was testing him and the sub to try and get a military contract.
Under unknown circumstances, V.E.N.O.M. managed to steal Brian the Brain from the BRC laboratory and took control of the sub, making it impossible for Bolt Research to make contact. They hooked the computer up in a wooden lodge near the Panama Canal and threatened to blow up the sub with a missile from the Switchblade, creating nuclear contamination unless they got full control of the Panama Canal.
Matt Trakker found out about the misbehaving sub firsthand while enjoying a water ski vacation in Panama. He contacted Joe, his contact at Bolt Research twice to get information about Brian and the sub. When Trakker managed to contact Brian, the Brain recognized Trakker's name as the man who gave the grant to create him. Trakker told Brian to sink the submarine, but Brian refused to destroy himself.
M.A.S.K. triangulated Brian's location and despite oposition from V.E.N.O.M., it was Dusty Hayes who managed to imobilize Brian by using Gator's freeze gun. As soon as Brian's Brain was deactivated, he lost control over the submarine and it surfaced. The various M.A.S.K. vehicles teamed up to tow the sub across the canal. Miles Mayhem attempted a final strike by launching a missile at the sub, but M.A.S.K. intercepted it in midair.