Ok, so after Nero destroyed Vulcan and almost destroyed Earth, Admiral Marcus realizes Starfleet is nowhere near prepared for the inevitable (he thinks) war with the Klingons. So he creates Section 31 to start researching weapons and designing more war-prepped ships, tech, etc. He also sends more starships out to "explore" but really look for new tech they can adapt for weaponry. So one of these ships finds Khan early. Khan wakes up automatically while the rest of the crew stays asleep (that's what happened in TOS, assuming the same thing happens here). Marcus agrees to let him and his crew loose in exchange for help with his little project, since Khan is such a great tactical mind and experienced warrior.
As the project comes to a close, Khan realizes Marcus has no intention of following through with his end of the bargain, so he sneaks his crew into these special torpedoes behind Marcus's back.
Now, the book makes it clear that Marcus had no idea the crew were in the torpedoes, and he didn't know anything was less than hunky-dory with Khan until the terrorist attack in London (I got the impression in the movie that Marcus knew they were in there and wanted Kirk to shoot them at Khan to blow up all of the supermen, but whatever).
So Khan's motivation is SUPPOSED to be to escape with his crew (and, to a lesser note, get revenge on Marcus). So he blows up Marcus's base, then waits for the bigwigs to convene at their "secure" location and kills all of them too. Then he escapes to Kronos, hoping for...what exactly? That Marcus will survive his attack and come after him along with the torpedoes and he'll find a way to take them back and take the ship? I guess? He seems to want both a ship AND his crew, which would make sense considering the Botany Bay was essentially worthless. And I guess Kronos makes sense, since he figured Marcus would want to get his war started anyways and show how important his new ship was.
Let's say that makes sense. I'll give it that one. So Marcus sends the Enterprise after him with the torpedoes, and Kirk threatens to use the torpedoes on him. So he surrenders, presumably thinking he'll get on the ship, escape, kill or get rid of the crew and wake up his crew. So what if Kirk had just followed his orders? The torpedoes WERE armed...we know that from the McCoy/Carol scene. Would him and all his crew have been killed when the torpedoes were fired and struck?
Well, let's say for sake of argument that Khan reprogrammed the torpedoes so that they looked like they were armed but they weren't, or that he had some plan to get his people off of them if they were fired before they blew up. So he'd get them off. He wouldn't get his ship, but he'd get the crew. Or maybe he assumed that a member of Starfleet would try to capture him like Kirk ended up trying to do because that's the LAW, and Starfleet follows the law.I don't think Marcus would've bothered with that, but whatever. Maybe he even assumed Marcus would do it in true Starfleet fashion, send a team to arrest him, bring him back for trial, and he'd escape and get his crew back all on his lonesome from wherever the torpedoes ended up. All of this is all a stretch (and some sloppy, SLOPPY writing) but we can maybe reason it away if need be.
But here's the part that I can't wrap my head around no matter how much I think about it. WHY did Marcus blow the Enterprise's warp core at the edge of Klingon space? If Kirk had made his decision to disobey his orders BEFORE the warp core blew, then you could assume that Marcus found that out and was trying to remove his options to force him to either use his torpedoes or give him time to get the Vengeance ready to come after the Enterprise.
But Kirk didn't make that decision until AFTER the warp core blew. So Marcus obviously intended to blow the warp core all along (the book indicates that the fact that the warp core shutdown happened is the major reason Kirk changed his mind, because he was afraid they couldn't escape if the Klingons came after him, and they had a better chance of avoiding them with stealth than torpedoes, so at least in the book, Marcus was a dumbass. In the movie, it looks more like Kirk had an ethical dilemma and decided to do the "right" thing by Spock and it had little to do with the core, so take that for what it's worth). What was the point of that? If Kirk followed his orders, and considering how pissed he was about Pike, Marcus could safely assume he would, then he's send off the torpedoes, blow Khan up, and go home. He'd probably get his war, Khan and his folk would be dead, the whole thing would be covered up, no problem. And if Kirk didn't follow his orders, then you blow the core. It just makes NO SENSE to me to blow it preemptively.
The whole situation can only serve two purposes in my book: 1. To up the drama and make the plot work so that the Vengeance can come get them; or 2. So that the movie ties into the comics, where they made a big deal about how Marcus has inside control of the Enterprise before this even happened. Either way, it has ZERO to do with the actual plot of the movie.
That was long, but I wanted to make sure I worked it out, lol.
There's other nitpicks - where the heck was the big starbase and allllll those ships when the Enterprise and the Vengeance were duking it out over Earth? You'd think Starfleet would have someone come over to check it out, even if they were missing the command crew after the attack. And you'd assume that they'd defend the Enterprise since they'd never seen the Vengeance before, and send over a crew with hand communicators or something to see what was going on. Oh, and if communications were down with Earth, how the heck did the Enterprise call New Vulcan? Earth was RIGHT THERE. But those are much more insignificant than the big one above.
Just my two cents.