(Full disclosure: I did not take the time to scan all of the existing challenges to see if this has already been issued - I'd be surprised if it hasn't actually but I wanted to get this written down before I forgot about it ... again!)
K/S TOS - The Wrath of Khan
Basic premise: Khan has triggered the Genesis wave and it is on countdown to detonation. Kirk & Spock are both on the bridge - knowing they won't make it unless ... What if Kirk, not hearing back from Engineering, decides to go there, leaving Spock in command and then Spock, knowing what Jim was planning, took the alternate lift to follow him, leaving Saavik (or Sulu) with the Con. Then, in Engineering, Scotty is collapsed, Bones is not there (yet), and just as Kirk starts to enter the reactor chamber, Spock nerve pinches him and places his katra with his T'hy'la. Kirk is completely immobilized but is aware of what is happening. Since they have been bonded for a long time (however long suits the author, but definitely well before the events of TWOK) the two minds/souls do not clash but Kirk's acceptance is mixed with horror and denial. From there, it is Spock who saves the ship and his T'hy'la - Bones, Scotty & other crewmen have to stop Kirk from following Spock into the chamber just as in canon.
I would like to see how different the story might have been with this twist and how things might play out differently from there.
Feel free to include Saavik/David.
The title is merely one I thought of - change it to suit the story that you develop.
Characters: Carol Marcus, Chekov, David Marcus, McCoy, Original Character(s), Saavik, Scott, Sulu, Uhura