Tobias is under a simulation that wires him to think Tris is the enemy and a stranger. He is a pawn under the real enemy's hand. They let Tobias control this with out interfering because they know he is under a sim. Tris fights Tobias and has a gun to his head ready to shoot. She then turns the gun around so it is facing her and sticks it in Tobias's hand. That takes him out of the Simulation because he can't get himself to shoot her. They then are in the inside and take down the program controlling everyone else and they win.