Spock (alternate reality)/Starfleet career/Enterprise first officer/John Harrison

The next morning, Scott informed them Harrison had used the confiscated transwarp beaming formula to flee to Qo'noS. Marcus gave the vengeful Kirk permission to hunt down Harrison, and allowed him to reinstate Spock as his first officer. Spock objected to Marcus's orders to execute Harrison from orbit with 72 experimental photon torpedoes, deeming it immoral to kill him without trial. Kirk listened, and decided to arrest Harrison instead. Spock was also suspicious of the weapons specialist Marcus appointed to the Enterprise, , and found no records of her serving on any ship.
Spock and Uhura joined Kirk's away team in a shuttle to Harrison's location. When they were attacked by a Klingon patrol, Harrison appeared and singlehandedly killed them all so he could be taken into Kirk's custody. In the brig, Spock and Kirk questioned Harrison, who only responded that they examine the torpedoes, as well as a set of coordinates. In the meantime, Spock learned Wallace was actually Marcus's daughter, who was using her mother's maiden name as a cover, and informed Kirk before he ordered her to examine the torpedoes. 
McCoy and Marcus opened a torpedo and found a man held in cryogenic stasis. Harrison revealed he was Khan Noonien Singh, revived and forced by Admiral Marcus to design ships and weapons for war with the Klingon Empire, and he had tried to smuggle away his fellow Augments but was forced to leave them after being caught. Marcus arrived in the and demanded Kirk hand over Khan, but Kirk refused, wanting Khan to stand trial and expose the conspiracy. During the confrontation between the two ships, the Vengeances weaponry was deactivated by Scott, who was on a leave of absence and had boarded the ship after investigating the coordinates given by Khan. Kirk decided to board the ship with Khan, given his knowledge of its design, but Spock protested, distrusting Khan. Kirk countered he was desperate and needed his help.
While Kirk and Khan boarded the Vengeance in thruster suits, Spock contacted his older counterpart on New Vulcan, asking for information on Khan. Although the older Spock had sworn not to further interfere with history, he warned Spock that Khan was the most dangerous adversary the Enterprises counterpart had ever faced. Spock ordered McCoy to remove the stasis chambers from the torpedoes, before Khan appeared on the viewscreen, revealing he had murdered the admiral and taken control of the Vengeance. He demanded the torpedoes in return for Kirk and Scott, so Spock obliged, but Khan began firing on the Enterprise. An unsurprised Spock had the torpedoes detonated, crippling the Vengeance.
The damage sustained to both ships caused them to fall to Earth. Spock strapped on his seat belt and ordered all emergency power to life support, demanding the crew evacuate, but they refused, wanting to go down with their ship. However, the Enterprises engines reactivated, preventing it from crashing. Scott asked Spock to come to the warp core, where he found Kirk had repaired it without putting on a suit to shield himself from radiation poisoning. Kirk said he wanted Spock to know why he'd saved Spock from the volcano. Spock brokenly replied "Because you are my friend." As Kirk died, Spock lost his Vulcan demeanor and screamed, "KHAN!"
He beamed down to San Francisco where the Vengeance had crashed, and pursued Khan with the intent of executing him. The two fought on automated floating barges, but neither the nerve pinch or mind meld had any effect on Khan. Uhura beamed down and fired several shots to stun Khan, while explaining they needed his blood to cure Kirk. Spock finally knocked out Khan and brought him to sickbay, where McCoy performed a blood transfusion.
Two weeks later, Spock greeted a conscious Kirk and McCoy in a hospital room, where he expressed gratitude "Jim" was alive.