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This post basically summarizes my basic analysis and summary of the motives of Cumberbatch's character in my movie, who is the main character of my fanfic.
Note: I also composed this more cryptic summary of the fanfic (although looking at the character listed underneath might already do the spoiling.)
POST into darkness. (SPOILERS, duh!) They say let sleeping dragons lie but there is always someone who is not listening. Awaken into a situation even more vile than before, it remains to be seen who will triumph last. The Cardassian Spy who gambles for everything or the one that thinks he has nothing left to loose ... Not beta-read (looking for one)
The movie often puts a fast pace before a clear narrative and a lot of what we find out about Khan's motivation comes from two sources: Himself and people who do not like him. Which makes both of the information unreliable.
For example, Alexander Marcus (Peter Weller) is a deranged, war-mongering admiral who is so wrapped up in his own justifications that we basically can see him lie with utter conviction. Old Spock gave information that was at least partially false (okay the younger self might have misunderstood) but it shows that he was biased as well - but I get into that later.
Khan himself can not be taken as being always truthful and accurate because even he can use a lot of the truth to convincingly manipulate the Kirk and Co, there is always the possibility that the bended it a little bit.
So what we actually see happen on screen paired with combining what is said by everyone would be the way to go.
What we do know
Section 31, Starfleet's (or should I say Admiral Marcus) cloak and danger organization found the Botany Bay*. Khan was then blackmailed by Marcus into building the Vengeance and other weapons for him using the still frozen crew. Khan managed to hide all 72 of them in long-range torpedoes.
He bombed the research facility to gain access to the beaming device, attacked the meeting of senior starfleet officers and went on to Kronos. A chance Marcus used to further his own plans by sending a patsy with the 72 torpedoes after him. Upon realising that the torpedoes were indeed there, Khan gave himself up and revealed what Marcus had done.
With Kirk's help he got onto the Vengeance, took over (killed Marcus) and had the torpedoes beamed upon board. Which did not turn out so great. Then after thinking that they had killed his crew, he crashes the Vengeance into Starfleet headquarters.
Discovered or part of the plan?
A great weakness of the plot is that while it works out - you got to wonder, how did this make sense from Khan's point of view? We can assume that the full de-frosting procedure takes time. It must take significantly more time then hiding them in those torpedoes. That still leaves the question, now they are in there, how does he get them out? Disappearing with 72 cryotubes or even bigger torpedoes is certainly not easy, even though Starfleet clearly sucks at security procedures.
My point is, Khan must have had a plan to get the torpedoes out. So are we really sure that he was discovered conveniently after he put the last of his crew into the torpedoes? I think he counted on Marcus being willing to use the torpedoes regardless. After all if Marcus anyway had no problems killing everyone, why endanger his facilities or take the effort to remove the crew? All Khan then needed to do was give a good reason to use them. So I don't necessarily think that he was discovered but did the bombing to set his plan in motion.
Calculating that if he went to Kronos, Marcus would jump at a chance to start his war. Also that Marcus would utilize the torpedoes hoping to get rid of Khan and the crew (thus the most incriminating traces of his schemes in one go). This being the real reason for the second attack on the gathered Admirals and Captains. It removed more senior people who might have opposed the "Let's bomb the Klingon homeworld" plan.
Given that most of starfleet is compromised by sane and very docile captains with good morals, it is not much of a stretch to think that he probably counted on whomever Marcus would sent not just to blindly bomb the planet.
There is one major hole in the plan
Most of what goes on can be attributed to Khan planning it this way by betting on Marcus' insanity and general attitudes among starfleet officers - but that must also have involved him knowing about Marcus showing up with the Vengeance. I think he probably wanted that ship for himself and his crew anyway. But how did he plan on getting onboard?
If not for Scotty arriving there just in time and having the skills to sabotage the ship, Marcus would have obliterated the Enterprise with everyone on board, including Khan and his crew. Yes, he gave the coordinates to Kirk - but it is an awful lot of coincidence and chance for him to broker on some unknown person being a) sent there in he first place, b) arriving in time, c) not be discovered, d) able to sabotage the ship.
edit: Seeing the movie again, I caught up on something else. Maybe the back up plan in this case was having Carol Marcus on board. From the look she gave him, then later in sick bay how he looked at her - they must have known each other. Then on the Vengeance before he attacks her, the way she talks to him seems to indicate that as well.
Was the teary eyed monologue just an act?
I do think that Khan does care about his crew, I just think part of it was an act. He could not very well say "I got rid of most of your senior staff so Marcus had better chances of getting his own schemes into motion?" After all in some shape or form he needed Kirk to help him onboard the Vengeance.
Given the fact that his crew's life was in danger**, that he definitely was willing to risk everything for them, that part was certainly not an act. Allowing Kirk to see that for a moment only helped his position. So I think the tears were genuine but they were used for the purpose of manipulation. If that make sense?
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There are a couple of more questions I want to get into in another post; Like what it might mean when he said to Marcus "You should have let me sleep" or Spock's statement about him engaging in genocide of his inferiors, not mention the question why he did go for the destruction of the Enterprise. But right now, I got to fight my headache.
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* Don't think it was mentioned by name in the movie, but if you have seen WOK or Space Seed you know, that this was the name of the ship. In TOS Space Seed episode, Khan is awoken when someone finds the ship, here it is always presented as if out since it is a re-boot as much as a alternate time line, it might indeed be what happened in this case that was a deliberate act by Section 31/Marcus.
** If Marcus was willing to murder loyal Starfleet officers for his agenda, then he probably would not have hesitated to simply kill a number of already condemned war criminals. Just as we can reasonably assume that Khan would not risk his crew in such a scheme if he saw another chance to remove them from Section 31's grasp.
(no subject)
I also think that Khan really does love his crew. He's good at manipulating and certainly was working on it in that scene, but the tear comes when he's facing AWAY from Kirk and company. So I think it, specifically, isn't really part of the manipulation - or at least not a planned part. He certainly could adapt his approach on the fly to make use of it afterward. Which is maybe what you mean?
As for the 'let me sleep' line, I guess I hear it through my attempt to make this Khan somehow make sense with Montalban's Khan. The biggest difference in their situations is that the original Khan, though stranded, did have his crew with him for those 15 years. This Khan has only been awake about a year, has been used and abused by Marcus/Starfleet, and is profoundly alone. So I I see orig!Khan's rage and desire for vengeance at Kirk being channeled here into rage and vengeance at Marcus/Starfleet, and made more bitter/less restrained by his lack of support. And the 'sleep' line indicates to me that he hates being alone so much that he'd rather be asleep with his crew than awake and aware of missing them - he values/needs his crew being with him even more than he needs to rule.
Cumber!Khan flips out more than orig!Khan, but first he's icier - probably working under Marcus made him learn to repress his outward anger so as to not make him more suspicious. Or so my thinky-thoughts go.
I didn't really like how they handled Khan's past in ST:ID - the one throwaway line. I wish it was more clearly established exactly what happened in this vision of the Trek 'verse - Khan claims he was a "peacekeeper," Kirk claims he ran around wiping out various groups, and what I can find online for the original canon describes him as a dictator more than as a genocide. So it's...blurry. What do you think?
(no subject)
I think that might have also played a role in this „teary eyed“ scene. His pain was real, the concern for his crew was real - the horrible notion that he might fail them and be alone - but the word he spoke were certainly chosen and even where he stood. I think that what makes that scene so haunting and has lots of people even routing for him. That this not being in charge affected him, can probably also be seen in how much he blooms in the film once he gains control. He liked being on top before but I think thanks to Marcus, he know really relishes in it.
As for being alone, he totally was, even if some of the Starfleet people were „nice“ working with John Harrison - they were the enemy to him. As proven by the original space seed episode he is not above caring for non-superhumans - but in this situation ... he probably only looked to use people.
I don't think he really knew Carol closely - if at all they might have met briefly or read reports as they worked in the same field. The admiral probably would have done his best to keep them apart. I do think that Khan migh thave made sure her interest in the torpedoes was there.
My theory on Spock's comment about Khan's parting in genocide of everyone inferior is that knowing how dangerous Khan was, the old Spock lied to his younger self. Make Khan seem like a total monster, so that young!Spock would do whatever necessary. I am sticking to that in my story. Not trying to paint Khan as a nice guy, he certainly kills people who are in his way or to further a plan - but I think he is a leader first and foremost - not an ethic cleanser. He did not want to destroy the Enterprise at the end because he thought of them as inferiors that needed to be removed, they were the only ones left that knew about his crew. By getting rid of them, he would buy time to wake up his crew and then take an account of the situation.
Otherwise that line is just the lamest attempt to paint a grey character black for the final show down.