I suggested something similar to another writer in a review, but I wanted to present my original idea to see if anyone wanted to take it on. I am currently crazy busy with a five-day-a-week internship, working a part-time job, and trying to get a pretty long fic off the ground, so I doubt I will have time to write out this plot bunny anytime soon. I figured I would give it up for adoption in the form of my first challange ever.
The concept starts out in the Abrams Universe after Into Darkness. The Enterprise is stopping at New Vulcan for a routine supply stop. Spock has discovered romantic feelings for Kirk after his brush with death, and has been confiding in Spock Prime about them for a while (how long is up to you). He can still be with Uhura at this point, but it does not matter. During the stopover, Kirk is attacked by a Vulcan terrorist. The attack is telepathic, and makes Kirk mentally trapped in the worst time in his life, in this case Tarsus.
The Vulcan healers do their best, but cannot do anything. Spock Prime then steps in. He knows Jim better than anyone, and manages to make his way into the mental world and contact Jim's consciousness. However, he discovers the healing might take months, so the Enterprise leaves with Spock (reluctantly) in command. With Sarek's help, Spock Prime goes into Kirks mind long term and participates in a narrative where he helps a teenage Kirk escape from Tarsus, and finally his own mind. What Spock Prime did not count on was Kirk falling in love.
Spock Prime cannot resist having his T'hy'la back, but he has his counterpart to think about, as well as his place in the universe. He also has to let Kirk go back to his ship at some point. He also wants Kirk to realize just how much nu!Spcook loves him, although Kirk is a tad clueless right now.
Bonus points for some mental/physical side effects for Spock Prime and a confrontation between old and new Spock's. The Spock you have Kirk end up with is up to the author.