Star Trek ITD – My Story Theory…
The Klingons find Khan, at some point during Nero’s 25 year wait for Spock Prime and the red matter. Probably the Narada‘s incursion sends the SS Botany Bay off course into Klingon space. And recall, Klingon’s know about human Augments. They’d already dealt with a whole bunch a century prior and because of such they’ve head ridges. At the time they wanted Augments of their own.
So the Klingon’s wake Khan - But only Khan. Khan wants his brother and sister Augments, his family to be woken as well, the Klingons refuse. They want him to take down StarFleet and a mutual plan is hatched. Khan will infiltrate the Federation and StarFleet as a member, besides he wants to rule Earth himself and might need the Klingons for that…
All this takes place when Kirk is a baby/kid.
Khan, now going by the name John Harrison as his real name will get him thrown in a brig if not executed, enters StarFleet, his intelligence is renowned (though, I think he holds back on his super strength… almost) and Section 31 takes notice. John Harrison never becomes a captain, but an intelligence officer which gives him access to many, many things. His moral compass appalled by StarFleet‘s and the Federations Prime Directive – Remember Khan likes control and order, in a word he likes doing, not passive action.
Moreover he needs to save his family, who are still held on Kronos my the Klingons. Its taken him decades to bring his plan to fruition. He learns about Robert April and how he took over the Enterprise because of his Section 31 connections and so takes that data for later use.
Next is to win some hearts and minds – Like say a Lt. Clark Terrell who happens to have a sick little girl. Mmm… Khan/Harrison knows something about DNA and so cures Lt. Terrell’s dying daughter. He needs him… To maybe upload the data that Khan stole from the data archive to the rest of the fleet?
I know there is a lot lacking from this, though I think I have the bare bones of the plot itself. Could be wrong. We’ll see soon, real soon now.