Imagine this:
We never see John Connor. At least, until the very end of the movie. You see, he's reclusive - the many, many attempts on his life by robits from the future have taken a psychological toll, so he lives on a submarine, a ghost leader of the resistance, urging all others to fight the good fight, and he's damned effective.
Marcus still appears, like so, coming out of the mud. But instead of getting picked up at the gas station, he and Kyle Reese fight some cannibals together. It's pretty slick - and Marcus teaches Kyle to drive. The focus of the film is on their relationship, like T-800 was to a young John. Eventually, Kyle still gets captured.
But Skynet has NO IDEA WHO THE HELL HE IS. A main complaint with the film is that Skynet hatches a lame attempt to kill John Connor by capturing Kyle Reese, when they could just... uh, kill Kyle as soon as they recognize him. Of course, many, many scenarios have since been created to validate why Skynet did what it did, and they make as much sense, but still.
In any case, Marcus's interactions with Blair are much more blunt. He saves her from wolves instead of rapists, and she offers him a FOTS - Fuck on the Spot. Which he declines.
When he is captured by the resistance, he is interrogated by John Connor - via radio, as John Connor is under the impression that Marcus is from even further in the future.
In any case, he escapes, and makes his way to save Reese - a child he has bonded with - and Star, that stupid fucking mute girl.
When he reaches Skynet LA, he finds something shocking.
A beach-side paradise. No joke. Skynet is taking humans and converting them into Cyborgs, giving them a life without pain or suffering. See, Skynet before Judgment day crunched the numbers and found that humanity was going to off itself in about 200 years, so it took proactive measures, killing the majority of the population and saving the others in order to give them a pain free life. Serena - played by Helena Bonham Carter - explains all this to Marcus. There's a neural net, a composite of shared memories processed by removing the brain and uploading it to a network, the step taken before one becomes a full cyborg. And then she gives Marcus the bad news - Star has already been terminated, and Reese has already had his brain removed.
Serena is distracted by an explosion, and Marcus jumps through a temporal field - Project ANGEL, what Serena was working on, also dabbled in time travel. Marcus goes back in time about 20 minutes, causes the explosion to distract her, and rescues Reese and star. A large ATV chase, with Reese at the wheel, ensues through the beach paradise, where they are chased by HK tanks and choppers.
They finally reach the marina, where a sub and thousands of Resistance fighters, surface, and fight the machines off. Connor steps off the sub, when Marcus notices among the crowd of survivors, Serena is watching. She blows off Marcus's arm, and shoots Connor in the gut.
The resistance, not knowing what the hell Connor looks like, doesn't really flinch, and they cart both Marcus and Connor off. Kate and Connor know he is going to die, and offer Marcus a choice - he can live as a cyborg, or as the new leader of the resistance, with John Connor's face grafted on. He elects to lead the resistance.
