You need to have Tron in your party. Right after you fought that other guy called Sark or something... you'll be fighting another battle, with the REAL MCP this time.
All you gotta do in attack the now-giant-Sark's legs and then when he kneels over, attack his head. He'll be stunned afterwards and then attack the ring/barrier/wall thing that's surrouding the MCP, when an opening is made, use the reaction command (with Tron) and mash the triangle button like crazy. Do that a few times and MCP will be down in no time. Oh, be careful of MCP's laser attacks. =)