James T. Kirk/Starfleet career/USS Enterprise/Year Three

Kirk became the first Federation starship captain to ever face a court martial, after he was accused of causing the death of Lt. Commander Benjamin Finney, the Enterprise records officer. Kirk employed Defense Attorney Samuel T. Cogley, and Kirk's former flame Areel Shaw acted as prosecutor at his trial, which was held on Starbase 11, convened by Commodore . Kirk was exonerated after Finney was discovered alive, having faked his death and the evidence implicating Kirk. ()
When Spock kidnapped his former commander, Fleet Captain Christopher Pike, who had been horribly crippled, and commandeered the Enterprise in 2267, he inadvertently jeopardized Kirk's command. After Spock locked the ship on course to Talos IV, Kirk was a member of a tribunal that tried Spock, the other members being Pike himself, and an illusion of Commodore Mendez. Spock's crimes were in violation of General Order 7 and were punishable by death. Once it was revealed that Spock's ultimate goal was to allow Pike, a Starfleet hero, to live a semblance of normality under Talosian illusion, Starfleet declined to prosecute the matter. ()
When the Enterprise passed through the Omicron Delta region, Kirk hoped to arrange for his crew (and himself) to take some badly needed shore leave. While Kirk and his landing party investigated a candidate planet to determine its suitability for that purpose, they were beset with manifestations of hidden desires they had. In fact, they had discovered the Shore Leave Planet, and advanced technologies which an ancient, enigmatic species had left behind. ()
On stardate 2124.5, a being calling himself "General Trelane (retired), the Squire of Gothos" waylaid the Enterprise. Though immensely powerful and troublesome, Trelane was revealed to be nothing more than a child of his species, and a badly behaved one at that. Kirk was put on trial, albeit this time in an illusory court, by Trelane. ()
Kirk made contact with the Gorn Hegemony and the Metrons on stardate 3045.6. Finding a Federation base on Cestus III destroyed and Gorn forces lying in wait, Kirk ordered the Enterprise to give chase to a Gorn starship that had been responsible for the attack, intending to destroy it. The pursuit took the two belligerents through Metron space. The Metrons, pacifistic but powerful, interrupted the engagement and declared both sides were savages.
Kirk and the Gorn captain were removed from their respective ships by the Metrons and deposited on a desolate planetoid, where the Metrons forced the two captains to fight each other, threatening to destroy the loser's vessel. Kirk was victorious, but refused to kill the Gorn. Kirk's act of mercy impressed the Metrons, who allowed both ships to go free. ()
On stardate 3192.1, the Enterprise was caught up in a "civilized" interplanetary war between Eminiar VII and Vendikar, whose engagements were fought only by computers, and marked "casualties" among the citizenry dutifully reported to death chambers. After the Enterprise was declared a target and the crew ordered to die, Kirk destroyed the Eminiar computers, forcing them to finally treat with their enemy – or face a war that would destroy their civilization. ()
The Enterprise discovered the , an ancient sleeper ship, on stardate 3141.9. The vessel carried a group of eighty-four genetically-engineered Augments from Earth's Eugenics Wars, kept alive in cryogenic freeze; twelve of these had died when their stasis capsules failed. Their leader, Khan Noonien Singh, seduced Enterprise historian Lieutenant Marla McGivers, revived his seventy-one surviving comrades, and attempted to steal the starship – before Kirk stopped him. Somewhat respectful of Khan's integrity and abilities, Kirk exiled Khan and his people on planet Ceti Alpha V, where the former tyrant would have a chance to "tame a world" without threatening others. ()
Under the euphoric, enervating influence of pod plants, the entire Enterprise crew mutinied, abandoning the ship for the planet Omicron Ceti III in 2267. Kirk was the last to fall under the influence, but his subconscious anger at the idea of leaving the ship rose to the surface, and broke the pod plant's effect. ()
Accompanied by Spock and McCoy, Kirk discovered the first known silicon-based lifeform, a sentient Horta matriarch, on the mining colony Janus VI on stardate 3196.1. ()
At the start of between the Federation and the Klingon Empire, Kirk and Spock met with the Organian Council of Elders personally and attempted to convince the Organians, who were apparently primitive, to accept Federation protection. Shortly after the planet Organia was subsequently occupied by Klingons, Kirk and Spock began conducting a guerrilla war against the Klingon occupation, but Organians abandoned their false humanoid forms and intervened, forcing an end to the interstellar war and imposing the Treaty of Organia. Organians predicted that, in time, the antagonistic powers would eventually become friends. In the end, Kor, frustrated by Organian interference that made battle against Kirk impossible, wistfully surmised, "it would have been glorious". ()
Responding to the Deneva colony having recently gone silent, Kirk found that a hive-mind of marauding flying parasites had killed his brother, George Samuel Kirk, and that the colony's remaining population was under their influence, causing mass insanity. McCoy and Spock were able to develop a method of killing the exotic creatures. ()
By this time in 2267, Kirk had finally settled on Ensign Pavel Chekov as the Enterprises regular navigator. ()
Kirk, Spock, and McCoy discovered Zefram Cochrane, the inventor of the warp drive, missing for 150 years, on a planetoid. An energy being Cochrane called "the Companion" had kept him alive and young all those years. At Cochrane's request, Kirk did not log the encounter. ()
Kirk diverted the Enterprise from an assigned ceremonial mission on Altair IV to on stardate 3372.7, in order to save his first officer from the dangerous effects of his pon farr mating cycle. In the presence of the Vulcan matriarch, T'Pau, Kirk was forced to participate in Spock's marriage ceremony. ()
A distress call led the Enterprise to the crippled after an ancient machine, deemed a "planet killer", had nearly destroyed that starship. While stranded aboard the nearly crippled Constellation, he and Chief Engineer Scott worked together to recover enough power and control functions to partially restore ship's functions. After Matt Decker, a Starfleet commodore who was now mentally unbalanced, made a suicide run with a stolen shuttlecraft, Kirk piloted the Constellation inside the machine, detonating the engines and destroying the device. ()
On the planet Halkan, a transporter malfunction swapped the Enterprise landing party with a corresponding landing party from a parallel "mirror universe" where a savage, oppressive, Terran Empire had replaced the United Federation of Planets. captained the , whose first officer was a ruthless, bearded . ()
After beaming down to the planet Gamma Hydra IV, Kirk, along with Spock, Dr. McCoy, and Scott were all exposed to a rare form of radiation poisoning from a rogue comet. The radiation caused the party to age very rapidly. Kirk's accelerated dotage forced Commodore Stocker, who was visiting the Enterprise, to relieve Kirk from command of the ship until Dr. McCoy discovered a cure. Standard hyronalin therapy, alone, was ineffective. It was not until Spock, Nurse Chapel, and Dr. Janet Wallace were able to concoct a new type of treatment based on an old-style adrenaline radiation therapy that Kirk and his party could receive an antidote for the poisonous radiation, and just in time for the captain to regain his ability to command and save the Enterprise from a heavy Romulan attack into which Stocker, whom Kirk had earlier dismissed as a "chair-bound paper pusher" but who had relieved him after an extra-ordinary competency hearing, had unwisely led the ship. After Kirk was cured, he managed to maneuver the Enterprise out of the Neutral Zone and away from Romulan ships via a bluff. ()