"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.
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.
The original ending. John Connor dies 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. Fan backlash prior to production meant the ending 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 outright blasted by everyone who heard about it.
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.