Just got back from seeing Star Trek Into Darkness.Fun movie and I'll probably do a formal review later. I'd suspected we'd be seeing Khan Noonien Singh again, since the way the reboot was handled (time-travel to the pre-original series era) meant that all the old plots could be redone again and Khan is one of the most beloved (if that's the right word) Star Trek villains. Given the complaints I'd heard about how redoing Star Trek II: The Wrath of Khan would be insulting to the original, I had the idea of making the famous enemies James T. Kirk and Khan allies this time around.
Alternate history is one of my hobbies and one of the terms used in the AH subculture is "butterfly" as a verb. Basically, events that happen after the point of divergence from our history are likely to be "butterflied" away. This is an allusion to the butterfly effect. The events of the Star Trek (2009) pretty much "butterflied" the entire Trek timeline after the arrival of the Romulan time-travelers, considering how many Starfleet characters from the original series were likely killed in battle with the Narada, Vulcan itself (with most of the Vulcan population) was destroyed, Kirk seems to have become captain much earlier, etc.
This meant the five year mission of the original series would not have happened as it did, which means either the Botany Bay isn't discovered or someone else finds it first. Since the Klingons were active in the region of space the Enterprise was exploring, there was a good chance they'd find it.
So here's what happens. The Klingons discover the Botany Bay, defrost the Augments, and essentially enslave them for some purpose (similar to how Admiral Marcus puts Khan to work for him in the film). The Star Trek: Enterprise TV series depicted some kind of virus derived from the Augments infecting the Klingons, so perhaps the Klingons want the Augments to assist them in dealing with that, or they simply want them to help with the Augment technology they'd captured. Starfleet learns of a group of humans apparently working for the Klingons and orders the Enterprise on a covert mission to destroy them. Kirk and friends end up rescuing the Augments and Kirk and Khan work together to foil whatever it is the Klingons are doing.
Then Section 31 shows up, acting on intelligence collected from Old Spock. They detain Khan and the Augments and for a helping of dickishness, Lt. Marla McGivers as well. Never mind that this time around, she hasn't done anything wrong. Khan manages to turn the tables and escape with his kindred (and Lt. McGivers as well). Bonus points if it's on the U.S.S. Reliant. This shows the Federation isn't nearly as utopian as it initially seems and might sow a rift between Young Kirk and Young Spock and Old Spock. It also gives Khan a modern spacecraft and allows him to be a recurring nemesis to the Federation and to our heroes (if he thinks they betrayed him). Plus it provides a roughly similar rationale for "Into Darkness"--the Federation has shown its darker side, our heroes are at odds with each other, the events of the film might kick off a Federation-Klingon war, and one of the most dangerous men in human history has now got a second chance to wreak havoc.
And although Benedict Cumberbatch did a good job as Khan, it would have been better to have an Indian (or someone who could more credibly pass as Indian, which Cumberbatch really can't) portraying him. Ricardo Montalban, the original Khan, was Mexican. Were I casting Khan for this film, I would have sought out Hrithik Roshan. He's the right ethnicity to play Khan and since he's a handsome fellow (I think he's a Bollywood sex symbol), it's plausible he could include sexual seduction (see McGivers in "Space Seed") in his bag of tricks.