James T. Kirk (alternate reality)/Starfleet career/Commanding the USS Enterprise/Year Two

<tabber>
|-| Demotion=
A year later, Kirk violated the Prime Directive on Nibiru, saving Spock's life from a cold fusion device detonation inside a volcano. During the rescue, the Enterprise was exposed to the primitive Nibirans, who began worshiping the ship as a god. Returning to Earth, Pike informed Kirk the Admiralty headed by would be sending him back to the Academy, and that perhaps he had been promoted too soon. That night, Kirk drowned his sorrows in a bar, when Pike appeared to reveal he had convinced Marcus to let him appoint Kirk his first officer, because he still had faith in the young man. As a result, however, Kirk was demoted to the rank of commander rather than captain.
|-| Pursuing "John Harrison"=The two then attended a summit, in the Daystrom Conference Room at Starfleet Headquarters, regarding the bombing of the Kelvin Memorial Archive in London. Marcus ordered a manhunt for the perpetrator, a rogue commander named John Harrison. Kirk analyzed surveillance of Harrison at the debris site, and questioned why Harrison bombed an archive for the information he needed. Kirk then realized Harrison would be aware protocol dictated such an attack would precipitate meetings like these: Harrison then showed up in a jumpship and opened fire.
Kirk wrapped a fire hose around a rifle and threw it into the jumpship's engine, causing it to crash. Before it did, Kirk saw Harrison glaring at him and then beaming himself away. Kirk returned to the conference room to find Spock with Pike, who had died of a chest wound, and mourned his friend's death. 
The next morning, Kirk was notified by Scott that Harrison had used a portable transwarp beaming device to escape to Qo'noS, the homeworld of the Klingon Empire. Kirk informed Marcus, who explained the Archive had actually been a Section 31 facility, which Harrison had needed to steal the beaming device from. Marcus reinstated Kirk's command and rank as captain, giving him permission to hunt down and execute Harrison, and allowed him to reinstate Spock as his first officer.
|-| Qo'nos=To execute Harrison, Marcus gave the Enterprise seventy-two advanced long-range torpedoes to bombard Harrison's location from orbit, and assigned weapons expert to the Enterprise. At a hangar, McCoy expressed his belief that Harrison was out of Kirk's league, while Spock protested executing Harrison without trial was immoral. Aboard the Enterprise, Scott protested about not being allowed to examine the torpedoes, and not having time to examine the ship's warp core, which was new but faulty. Kirk accepted Scott and Keenser's resignation, and appointed Chekov to replace Scott. Dejected, Kirk decided to listen to Spock and Scott's advice, and announced they would find Harrison and bring him back for a tribunal.
Before reaching Qo'noS, the Enterprises warp core broke down, so Kirk took an away team with Spock, Uhura, and Hendorff, disguised as K'normian arms dealers, to find Harrison in a K'normian trading ship. 
Shortly after acting captain Sulu sent a targeted comm burst from the Enterprise to Harrison's location, Kirk's ship was attacked by a Klingon patrol, and despite maneuvering it through a narrowing gate, the away team found themselves surrounded. Kirk allowed Uhura to exit the ship and negotiate with the Klingons in their native language, but they refused to listen and tried to kill her. Before Kirk and Spock could come out firing phasers, Harrison appeared and single-handedly killed all the Klingons. Kirk accepted Harrison's surrender, but spitefully punched him, only to find his continuous blows had no effect on him.
|-| Uncovering a conspiracy=
In the ship's brig, Kirk and Spock interrogated Harrison while Bones took a blood sample, which he studied by injecting into a dead tribble. Harrison only responded by giving Kirk a set of coordinates, and advised the captain to open one of the torpedoes. Spock informed Kirk that Wallace could examine the torpedoes, and also told the captain that he had learned she was actually Admiral Marcus' daughter, a fact Spock had chosen to reveal at that precise point because he felt the information had just become relevant. Kirk also called Scott via a communicator and asked him to investigate the coordinates.
McCoy and Carol Marcus took a shuttle to a meteor to examine a torpedo, but McCoy accidentally activated the countdown and trapped his hand in the device. Kirk ordered to beam them up, but was warned by Spock that beaming up McCoy would also beam up an exploding torpedo. Fortunately, Kirk avoided losing his friend when Carol deactivated the device with less than three seconds to spare. The torpedo finally opened up, and the two officers found it contained a man in cryogenic stasis.
Kirk interrogated Harrison again, who explained he had placed people in torpedoes to smuggle them before he was caught. He revealed he was actually the infamous Khan Noonien Singh, recruited by Admiral Marcus under a new identity to design weaponry and ships for war against the Klingons, and that the frozen people were his fellow Augments, whom the admiral had held hostage. Marcus suddenly showed up in a ship, the , demanding Kirk hand over Harrison. Kirk revealed he knew the truth, and defied the admiral by having Sulu warp the Enterprise back to Earth, where Khan would stand trial and expose the conspiracy. However, the Vengeance was capable of catching up with the Enterprise in subspace and fired on the ship, halting it as it arrived near Earth and the planet's moon.
After Carol tried to bargain with her father but was simply beamed by him over to his ship, Kirk tried to hand himself over to protect his own crew, but Marcus explained he had no intention of letting anyone in on the plot survive. Before the Vengeance could finish off the Enterprise, its weaponry suddenly deactivated. Scott called Kirk, explaining he had stowed away aboard the Vengeance at the coordinates given by Khan, buying them some time. Kirk, realizing Khan had designed the ship, allied himself with him, and the two donned thruster suits to fly over and commandeer the vessel. Khan's formidable strength was an asset in dispatching any guards they encountered, but Kirk was suspicious of Khan's motives and ordered Scott to shoot him unconscious later.
When they reached the bridge, Kirk confronted Marcus over his betrayal of Starfleet's ideals. However, Scott's attempt to stun Khan did not affect him, and the Augment tackled Scott and Kirk before proceeding to kill Marcus and take the command chair. Khan ordered Spock to hand over the torpedoes, which he complied with, and in return he beamed Kirk, Scott, and Carol into the Enterprise brig. 
Khan then turned on Spock, bombarding the Enterprise once more. Spock, who had the cryopods removed from the torpedoes, ordered them to be detonated, severely crippling the Vengeance; the shockwave caused both ships to be pulled by Earth's gravity. Kirk and Scott ran to the warp core, trying to avoid falling to their deaths due to the Enterprises failing artificial gravity.
|-| Death and resurrection=
Once they reached the Enterprises warp core, Scott warned entering it would flood the chamber with radiation, but as there was no time to put on a containment suit, Kirk knocked out Scott and secured him with a seat belt before entering the warp core. Kirk knocked the central component back in place, restoring power to the engines and preventing the Enterprise from crashing. 
Meanwhile, Khan crashed the Vengeance into Starfleet Headquarters in San Francisco. Scott woke up and called Spock to come to the area outside the warp core chamber, where Spock saw Jim dying from radiation poisoning. Jim bid goodbye to his friend, displaying the Vulcan salute with his hand on a glass door, then died. He heard the voices of his father, mother and Pike as he neared death.
Following decontamination, Kirk was taken to the Enterprises medbay, where McCoy and others silently mourned the loss of their captain. McCoy noticed the tribble he had injected with Khan's blood had come back to life, and realizing how to save Kirk's life, ordered his body be placed in a cryotube to preserve his brain functions. Spock and Uhura beamed down and apprehended Khan, enabling McCoy to create a serum from Khan's blood, which resurrected Kirk. However, the effects of the serum left Kirk unconscious for two weeks, after which he awoke in Starfleet Medical and was greeted by McCoy and Spock.
</tabber>