When you get to the level where all the troopers (blue/multicolored Mils with the wings) just keep coming at you, keep lobbing EMP grenades at them until they get trapped. Then, hijack one of them to get into the center building. Press the hand button on the wall. Then, exit the trooper (Scatter Blasters work best against them). Get into the tank after getting the energy cells. Then, just run straight through the barred/fenced area and just keep going to complete the mission.