I’ve seen a few wonderful ‘if only they’d done this’ type theories related to Benedict Cumberbatch and Khan, so I’d thought I throw my own out there.
Same general story line except ‘John Harrison’ is Joachim. After working for Marcus, Joachim learns the truth- Khan was woken first, and when he refused to do Marcus’s bidding, he was killed. This is Joachim’s motivation for the bombings- personal payback for killing his leader and holding the rest of the crew hostage.
Movie is same until we get to the scene in the brig between Kirk and Joachim. It’s basically- we are the same. We are both seeking vengeance for our commanding officer. We have both killed innocence people. We both owe so much to the men who brought us here. Really hammer in the Khan and Joachim vs Pike and Kirk parallels.
They’ve reached an uneasy understanding. Cue battle/confrontation with Marcus; Joachim is integral to their successful getaway.
They hide to regroup. They realize that Marcus could not possibly have acted alone and so they try to find who else is involved. In their research, Uhura discovers that Khan is not really dead! OMG a plot twist!
They also discover Marcus has branded them outlaws, and the rest of Starfleet is looking for them. With nowhere else to go, they search for Khan, because he has the proof they need to reveal Marcus’ evil plans. They find Khan, and Khan is justifiably paranoid over anything related to Starfleet. Joachim is clearly on Khan’s side, but argues for Kirk. We in the audience worry about betrayal.
Khan has the info, but won’t give it up until he has his crew back; Kirk won’t give the crew back until he has the proof. Stalemate. Kirk and Khan have a talk where we get Khan back story and they quote literary works at each other. Unsurprisingly, the literary quotes are quite arousing.
Before anything can be decided a Starship shows up. It’s half the size of the Enterprise, so Khan just wants to destroy it. That’s not going to happen, and Khan is pissed at their lack of savagery.
But good news! It is Captain One’s ship. Spock pulls Kirk aside- she was Pike’s first officer for 10 years, Spock served under both as science officer- let Spock take care of this. They do some fucking wonderful eye talking and we really see how awesome they can be together here. They separate and Spock relives Kirk under some Starfleet regulation concerning treason! And it’s hot.
And the crew is like WTF? Joachim and Khan are pissed and they look like they are conspiring too. Spock talks to Captain One, and it’s full of glorious Vulcan bullshit and ‘not lies’ and he convinces Captain One to give them time.
Except too late! Because Marcus has shown up! He quickly tries to dismiss Captain One’s ship, but she’s rightly suspicious because Marcus is not exactly following protocol either.
Meanwhile, Khan and Joachim are doing their own thing which involves waking their crew up and taking over the Enterprise. Enterprise ends up firing on the other ships, and Marcus uses this to take out One’s ship.
Battle, Kirk dies. Khan and Joachim kill Marcus and attempt to take over his ship. Captain One makes a last moment save the day and they recapture Khan and Joachim.
As Spock prepares to take them back to Earth, Khan reveals they can save Kirk and all they want in return to be left alone. Spock makes the deal, Kirk is saved and Khan and his crew are dropped off on the fifth planet in the Ceti Alpha star system.