The compound is suddenly attacked by a Harvester which grabs Virginia and a few others. Marcus and Kyle try to escape but are followed by Moto-terminators and an aerial HK. The Moto-terminators are destroyed in the chase but Kyle and Star are captured by the Harvester. The Resistance sends a couple of A-10 Warthogs which are shot down by an HK.
Marcus locates downed pilot Blair Williams (Moon Bloodgood) and they make their way to John's base, but Marcus is wounded by a magnetic land mine. Attempting to save his life, the Resistance fighters discover that he is in fact a cyborg with human organs, a mechanical endoskeleton, circuitry, and a partially artificial cerebral cortex.
Marcus believes himself to be human, demanding to be released so that he can save Kyle from Skynet, but John orders his destruction. However, Blair releases him and helps him to escape from the base. During the resulting pursuit Marcus saves John's life from Skynet hydrobots, and the two form an alliance. Marcus will enter Skynet's headquarters and attempt to disable its defenses so that John can rescue Kyle.
John demands that Ashdown delay the attack so that he can rescue Kyle and the other prisoners, but Ashdown refuses and relieves John of his command. However, John's soldiers remain loyal to him and he sends a radio broadcast asking the other Resistance fighters not to attack Skynet.
Meanwhile, Marcus enters the Skynet base and interfaces with the computer, disabling the perimeter defenses and allowing John to infiltrate the cell block and release the human prisoners. The Resistance's disabling signal is revealed to be a ruse, and the command submarine with the Resistance leaders aboard is destroyed by a Hunter-Killer.
Marcus discovers that he was created by Skynet and has unwittingly fulfilled his programmed mission to lure John into the base to be killed. He tears out the hardware linking him to Skynet and leaves to assist John in battling a T-800 model 101 Terminator.
John is mortally wounded during the fight, but succeeds in destroying the Skynet base by rigging several Terminator nuclear power cells to an explosive, detonating them as he, Marcus, Kyle, and Star are airlifted out. Kate attempts to save John's life, but his heart is too damaged.
Marcus offers his heart for transplant, sacrificing himself to save John. Recovering, John radios to the other Resistance fighters that though this battle has been won, the war is far from over.