"The future is not set. Iíve been told I said that once. Many years from now. It was a warning. That I was going to hell. But if I fought hard enough, I could escape. I believed it for a lifetime. Now I pray I was wrong. Because now I am in hell. We all are. And the future I used to dread is the only hope I have left."
The original cut of the film included a topless scene when Blair and Marcus are warming themselves by the fire. Director McG said that it was meant as a Shout-Out to Kelly McGillis' topless scene in Witness, but that it ultimately felt exploitative and would have flouted a PG-13 rating. The scene is reinstated in the director's cut Blu-ray.
A longer third act, that had John and Kate having a longer conversation before he leaves on the mission to rescue Kyle, appearances by T-700's, more footage of Marcus infiltrating Skynet, prisoners escaping during the attack, the T-800 trying to use the T-600's minigun and Kyle burying Marcus and finding Sarah's Polaroid in John's jacket.
Franchise Killer: The second one within a decade; the plans for any future endeavors with this incarnation vanished at some point and prompted another reboot that reset the Terminator playing field altogether; Bale was obviously not invited back, but Schwarzenegger was.
Stan Winston was intended to have a cameo as a prisoner who was fighting a Hydrobot in the Skynet research facility, but this was scrapped due to Winston's worsening health.
In a proposed ending, John Connor would die from his injuries and Marcus and Kate decide to honor his memory by letting "General John Connor" be a legend, via Marcus assuming Connor's identity. This ending was blasted by everyone who heard about it after an internet leaking, and supposedly McGs himself found it thoroughly wrong upon reading it, so it was changed for the theatrical version.
There was a second alternate ending where Marcus (who has had Connor's skin surgically grafted to his own so he can continue leading the Resistance) wake up, turn evil and kill everyone in his hospital room, including Kyle, Star, Kate and Barnes. It got as far along as having concept art drawn up for it, but was even more hated than the former and was eventually discarded.
An entirely different third act was written featuring a group of hybrids led by a cyborg Serena Kogan revealing themselves as controlling Skynet in order to create a new, superior mankind. Some scenes were shot and are contained in the DVD, but the production team ended up eliminating this storyline and reshooting the act because it was felt as too derivative and out-of-character with the franchise.
The submarine commanded by Ashdown was originally going to be destroyed by an underwater Harvester and not by a simple missile.
Had Arnold Schwarzenegger not given permission for his likeness to be used for the T-800 that attacks John Connor in the factory, the plan was to have Connor shoot the T-800's face off as the camera panned up.