Marcus manages to escape the Resistance hideout with the help of Blair. Connor catches up to him, but gets into trouble from a couple of the hydro-eel machines. Marcus saves his life. Reluctantly, Connor lets him go to get into the Skynet HQ and find Kyle Reese - and signal him with some type of ipad when he's ready.
Marcus presents himself to the Skynet sentry robot - which scans him, and then lets him through. He traces the cell for Reese and sends the info to Connor, and shuts down the sentry.
Connor blasts out some Guns n Roses to attract a local motorbike machine, and then takes it over to ride over the Golden Gate Bridge to Skynet Central.
Inside, Connor tries to find Reese and releases the other prisoners.
Marcus gets a make-over from Skynet, and is presented with the face of Helena Bonham Carter to help answer his questions. He learns that he was cryogenically frozen, and his body was later passed over to the US Air Force. He is an experimental new type of Terminator, and his role was to bring Kyle Reese and John Connor to Skynet Central to be destroyed. He also learns that the shut-down code was a ploy - and has only broadcast a signal of the submarine's location. Meanwhile, a HK flies over and blows the resistance leaders out of the water.
But the machines haven't reckoned on Marcus's strong heart and human willpower - Marcus takes the chip out from his head, and goes to help John.
Meanwhile, John has been led to a cell with a T-800, in the form of Arnie, waiting for him. There's a monumental battle, and in the middle of it John also manages to find Kyle and little Star. They stumble on a T-800 factory, and a handy little table full of fuel cells that they rig to blow.
Marcus turns up, finally, to lend a hand. Connor pours molten metal onto the Terminator's head, and then freezes him ... but he still survives. Connor is stabbed through the heart, but Marcus manages to tear off the T-800's head. He picks up Connor, and they make it to the choppers. They blow the place using the rigged nuclear fuel cells as they fly away.
On dry land, Connor is dying. Marcus volunteers to use his own heart to be transplanted into John - to earn his second chance.
As it ends, a healed John is now the leader of the resistance - and in a downbeat message tells his people that although they have won the battle, they still need to win the war ... as there are a lot of other Skynet facilities all across the world.