James T. Kirk (alternate reality)/Starfleet career/Commanding the USS Enterprise/The five-year mission

Nearly a year after his death and resurrection, Kirk presided over the rechristening ceremony of the Enterprise and a memorial service to those who lost their lives in terrorist acts committed by Khan, before setting off on Starfleet's first five-year mission. ()
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|-| Vastness of Space=Three years later, Kirk was helping to negotiate peace between the Teenaxi Delegation and the Fibonan Republic, working as a neutral representative by presenting the Teenaxi with a dismantled weapon as a token of peace. Suspicious of the Fibonans, the Teenaxi attacked Kirk – though due to their diminutive stature, Kirk was mostly unharmed and was quickly beamed back to the Enterprise by Scotty.
In his captain's log following the mission, Kirk expressed his frustrations with life aboard the Enterprise this far into its mission, stating he felt as though life had become "episodic." Near his thirtieth birthday, Kirk confided in McCoy over a drink, divulging that he now questioned his own motives for having joined Starfleet, as he had done so on Pike's dare, rather than because of a strong belief in the organization on his own behalf. Kirk was further upset by the fact that he would be turning one year older than George had been at the time of his death.
Due to these frustrations, Kirk applied for a promotion, seeking the position of vice admiral at Starbase Yorktown, when the Enterprise docked there for resupply.
|-| Loss of the Enterprise=
After Kalara arrived at Yorktown and claimed her ship had crashed on planet Altamid in the Necro Cloud, Kirk volunteered the Enterprise for a mission to rescue the survivors. Once the craft traversed the unstable nebula, a massive cluster of unidentified ships was detected, approaching the Enterprise. Kirk quickly realized something was amiss and raised the shields before the oncoming Swarm ships began to dismantle the Enterprise, causing multiple hull breaches and severing the nacelles. 
Kirk discovered the enemy was seeking the weapon he had tried to present to the Teenaxi, so he gave the artifact to Ensign Syl before the leader of the Swarm, Krall, could steal it. Realizing the ship's destruction was imminent, Kirk ordered the Enterprise crew to abandon ship. Kirk then attempted to execute a saucer separation, so the saucer section could safely land on the surface of Altamid. Kirk, however, ran into Krall and the two fought, but Uhura finally managed to sever the saucer section, sending Kirk to the surface of the nearby planet.
|-| Altamid=
On the planet's surface, Kirk landed near where Chekov and Kalara also landed. Furious, Kirk confronted Kalara, realizing she had known the Enterprise would be attacked. She revealed Krall had kidnapped her crew and threatened to kill those personnel, unless she helped. Realizing they needed to locate the rest of the survivors from the Enterprise, the three went to the site where the vessel's saucer section had crashed, and they scanned for crewmembers there. 
Kirk went to where he claimed to have left the weapon but was attacked by Kalara, who revealed she had been working for Krall all along and proceeded to contact him to let him know she had the weapon. Kirk, however, deceived her, having Chekov trace her communication to Krall. They were both attacked by his troops but escaped by activating the Enterprise thrusters, causing an explosion which in turn killed Kalara and thrust Kirk and Chekov through the air as they made their getaway.
The next morning, Kirk and Chekov walked into one of multiple traps prepared by Jaylah, a scavenger who was living on the planet, but they were freed after Scotty told her they were friends of his. Jaylah revealed she had made the wreckage of a 22nd century Federation starship – the – her home and, using the scanners, Kirk was able to locate Spock and McCoy, and beam them to the ship before Krall's drones were able to kill them. 
Kirk helped treat an injured Spock, while he revealed that the weapon had come from Altamid. Using the trace from Kalara's communication and pinpointing it with a Vulcan amulet Spock had given Uhura, Kirk's team was able to learn the exact location of their former shipmates and formulate a plan to not only rescue them but also stop Krall before he attacked Yorktown.
Using a motorcycle from the Franklin and holographic technology from Jaylah, Kirk managed to distract Krall so that Spock and Jaylah were able to escape with the rest of the surviving Starfleet officers. Once they were all aboard the Franklin, Kirk, at the last second, managed to rescue Jaylah and get her back to the ship. While Krall left for Yorktown, Kirk and the crew followed on the Franklin.
|-| Saving Yorktown=
When they arrived at Yorktown, Krall had nearly penetrated the base's defenses. Spock and Scotty realized they had to disrupt the communications between the drones in order to prevent the attack. As a result, Kirk ordered McCoy and Spock to transport onto one of the ships, in order to hack into the Swarm's frequency using a music player from the Franklin. They sent out a classical song over the frequency, rendering the drones unable to cooperate with each other and causing the destruction of all but three of the ships, one of which was being flown by Krall. 
The Franklin pursued his ship into the base and was able to block Krall's attack, causing him to crash into the Franklin, presumably killing him. Kirk searched the ship with Uhura, for confirmation, but during the search, Uhura discovered a recording of the original Franklin crew and deduced from the footage that the captain of the ship, Balthazar Edison, was Krall. By looking at his file, they discovered he had been a soldier who fought during the Xindi and the Romulan Wars, after which he had been given command of the Franklin. He had slowly started to despise the Federation's views and had slowly gone insane in the century after the ship went missing.
Scotty and Jaylah realized that Edison was going to release the weapon in the base's ventilation system, killing the base's inhabitants. Confronting the now-disfigured Edison in the ventilation hub, Kirk revealed to him that he knew who he was. Kirk also tried to persuade Edison that he was underestimating humanity and that the Federation was a cause of good. 
While the hub lost gravity, Kirk fought Edison, seized the bioweapon from him, and attempted to eject it into space by opening an airlock. Kirk was attempting to open it when Edison regained his strength; he continued to fight Kirk but was ultimately ejected into space with the weapon, which then killed him. Kirk was nearly sucked out as well but was spared by the timely rescue of Spock and McCoy. Kirk and Commodore Paris then closed files on the Franklins late crew.
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