The Boss after the brain computer has the Wave Motion Cannon. Once you start, run at him at an angle and jump kick the gun out of his hands -- he will fall down. While he is on the ground, run over to the gate with the two fallen guards on each side. Go to the right and pick up the Hypo. Use it, and when you are super charged go after the Boss. This should make quick work of his health. If he has any health remaining, just use combos on him. Note: Do not let him get the gun.