- Stardate 2712.4 (approx. 27 January): In search of Nurse Chapel's fiancé, renowned exobiologist Roger Korby, the Enterprise visits the icy planet Exo III, where Korby has discovered an ancient machine which allows him to duplicate any living person with an android replacement. Korby plans to use the machine to spread controlled androids throughout the Federation, and replaces Captain Kirk with such a duplicate in an effort to take over the Enterprise.
- Stardate 2713.5 (approx. 28 January): After discovering what appears to be a duplicate of the planet Earth, Captain Kirk and his landing party find a population ravaged by a strange disease, which only children appear to have survived.
- Stardate 2715.1 (approx. 29 January): While on a re-supply mission to a rehabilitation colony for the criminally insane, the Enterprise crew discovers that the chief doctor has been using a device which destroys the human mind. Captain Kirk and Dr. Helen Noel, down on the planet, must deal with the problem up close and personal.
- Reference Stardate 2/0902: The Nelson class scout U.S.S. Menke, operating along the rimward frontier, is listed as missing after failing to make a scheduled report. The Nelson class scout U.S.S. Stuart conducts a two-month-long search without success.
- The Organians decide to learn whether Humans and Klingons can live and work together. They select Sheridan's World as the site of an experimental colony composed of both Humans and Klingons. Should the project succeed, the Organians will consider lifting many of the restrictions to developing other worlds in the region.
- Stardate 2817.6 (approx. 7 March): While visiting an old friend, Kirk suspects a Shakespearean actor may actually be the murderous former governor of Tarsus IV. Kirk invites the acting troupe aboard the Enterprise in order to investigate, but soon assassination attempts are made on Kirk and another crewman who were eyewitnesses to the murders.
- Stardate 2821.5 (approx. 8 March): Spock and a scientific party are sent to study the Murasaki 312 quasar aboard the Shuttlecraft Galileo. During the survey, the Galileo is forced to make an emergency landing on the planet Taurus II, where the crew fights the planet's dangerous inhabitants. As the crew begins to make repairs, Scotty determines that the shuttle does not have enough fuel to reach orbit carrying all seven passengers, and Spock must contemplate leaving some of his fellow crew behind.
- Reference Stardate 2/0904: A convoy of six Cochrane class colonial transports, plus escorts, is listed as missing after failing to arrive at its destination of New Deimos. Some later believe the Gorn Hegemony may have been responsible, but no evidence supports the allegation.
- Stardate 2947.3 (approx. 23 April): Captain Kirk is placed on trial for negligence after a crewman is killed during a severe ion storm. Kirk maintains that his actions were proper and should not have led to the officer's death, but the evidence seems strong against him.
- Stardate 3012.4 (approx. 17 May): Spock hijacks the Enterprise to take his crippled former captain, Christopher Pike, to the forbidden world of Talos IV. He then demands a court martial, which he uses to tell the tale of Pike's captivity on the planet years earlier. After witnessing the Talosians' capabilities of mental illusion, Captain Kirk realizes that Spock intends to return Pike to the planet to live a life of illusion, unencumbered by his crippled condition.
- Stardate 3018.2 (approx. 19 May): Two powerful aliens threaten the well-being of the Enterprise and her crew with their apparently magical powers.
- Stardate 3025.3 (approx. 22 May): Captain Kirk orders shore leave for the Enterprise crew on a seemingly uninhabited planet in the Omicron Delta system. The landing parties begin to see strange sights, such as a White Rabbit a la Alice in Wonderland, Don Juan, and a sword-wielding samurai. Also, Kirk sees (and fights) an image of Finnegan, a rival from his Starfleet Academy days. Spock discovers that the planet seems to be drawing a large amount of energy from the ship's engines, placing the Enterprise in danger.
- Stardate 3045.6/Reference Stardate 2/0801.24 (approx. 29 May): The Enterprise comes under attack by unknown aliens while investigating the near destruction of the Cestus III colony. While chasing the aliens into unexplored space, both ships are captured by the powerful Metrons, who force Kirk and the Gorn captain to trial by combat: the winner's vessel will be set free, while the loser's ship will be destroyed.
- Reference Stardate 2/0906: Lieutenant Commander Willard Decker, a helmsman/weapons officer, receives a short-term shore assignment on Delta IV. Meanwhile, approximately 200 colonists arrive from the Federation and the Klingon Empire at Sheridan's World, under the direction of the Organians.
- Stardate 3087.6 (approx. 13 June): While orbiting an apparently dead planet, the Enterprise seems to experience a strange moment of "nonexistence". Captain Kirk discovers a man named Lazarus on the planet below, who claims the effect was caused by his "enemy," revealed to be an insane version of Lazarus from the devastated world, while the sane Lazarus is from an alternate dimension. The sane version of Lazarus asks for Kirk's help in defeating his counterpart.
- Stardate 3113.2 (approx. 23 June): After accidentally traveling back in time to 1969, the Enterprise rescues U.S. Air Force Captain John Christopher from his crippled fighter jet. The crew struggles to return to their own time, while simultaneously returning Christopher to his, removing his knowledge of the future and all record of contact with the Enterprise.
- Stardate 3134.0 (approx. 30 June): After accidentally overdosing on a powerful stimulant, Dr. McCoy becomes unbalanced and disappears through the Guardian of Forever, a newly discovered time portal on a remote planet. Kirk and Spock follow after learning that McCoy somehow changed history. Arriving in 1930, the duo meet Edith Keeler, a New York social worker who gives them a place to stay. As the days pass, and McCoy is nowhere to be seen, Kirk finds himself falling in love with Keeler... but Spock discovers that Keeler must die to restore the timeline.
- Stardate 3141.9/Reference Stardate 2/0712 (approx. 3 July): The Enterprise discovers an ancient sleeper ship, the S.S. Botany Bay, which escaped from Earth's Eugenics Wars in the late 20th century. The genetically engineered passengers, led by Khan Noonien Singh, attempt to seize control of the Enterprise. Khan and his followers—including Lieutenant Marla McGivers, the Enterprise's historian, who colluded with Khan in his attempt to seize the ship—are left to colonize Ceti Alpha V, in lieu of court martial or formal rehabilitation.
- Stardate 3156.2 (approx. 9 July): The Enterprise discovers a population on planet Beta III that is controlled by a powerful being called Landru. While investigating, Captain Kirk and his landing party are taken captive and discover that the Enterprise crew will be the next to be "absorbed" into Landru's control.
- Stardate 3176.0 (approx. 16 July): The Starfleet Corps of Engineers ship U.S.S. Lovell NCC-470 is dispatched to Beta III to examine the Landru computer.
- Stardate 3192.1 (approx. 22 July): On Eminiar VII, the Enterprise finds a civilization at war with its planetary neighbor, Vendikar. Unable to discern any signs of battle from orbit, Captain Kirk and Ambassador Robert Fox lead a landing party to the surface where he discovers the entire war is fought by computer. Even though the war is simulated, citizens who are listed as virtual casualties still report to termination booths to be killed in reality. After the Enterprise is "destroyed" in an attack simulation, Kirk must fight to keep his crew from death.
- Stardate 3196.1 (approx. 23 July): Dispatched to the mining colony on Janus VI, the Enterprise is tasked to investigate rumors of a strange, subterranean creature responsible for destruction of equipment and the deaths of fifty miners. Kirk and Spock discover a silicon-based life form, a Horta, which lives in the surrounding rock. After Kirk and his Vulcan first officer find the strange creature, Spock performs a mind meld, discovering the reason behind the Horta's attacks.
- Stardate 3198.4/Reference Stardates 2/0801.06-2/0801.09 (approx. 24 July): When representatives from the United Federation of Planets and the Klingon Empire fail to reach a peaceful resolution to their differences, Klingon warships invade Federation space. The Enterprise is ordered to protect Organia, a peaceful planet located near the Klingon border. Captain Kirk and Lieutenant Commander Spock beam to the surface to warn the Organians about the Klingons, but soon thereafter, a Klingon battle group led by Commander Kor seizes the planet, forcing the Enterprise to abandon the Kirk and Spock on the planet. The natives protect the two, even as Kor orders mass executions of the Organian people. As both Federation and Klingon fleets converge above the planet, Kirk and Spock execute a daring raid on the Klingon headquarters in an effort to destabilize their control over the planet. The Organians suddenly intervene, immobilizing all Federation and Klingon ships throughout the galaxy. They impose the Organian Peace Treaty, thus averting another war between the two powers. The Organian Treaty Zone is established by negotiation over the next three months, resulting in important changes in the Klingon/Federation border, yielding new territorial gains for both sides. Although both sides honor the treaty, the fate of various "orphaned" worlds in the newly-established Klingon Neutral Zone remains unresolved.
- Stardate 3198.4 (approx. 24 July)
- Stardate 3211.7 (approx. 29 July): Captain Kirk, Chekov and Uhura are kidnapped by powerful disembodied aliens and forced to fight in gladiatorial contests for the aliens' gambling entertainment.
- Stardate 3219.4 (approx. 1 August): A shuttle crew from the Enterprise encounters a castaway who appears to be Zefram Cochrane, the inventor of warp drive and his mysterious alien companion.
- Stardate 3287.2 (approx. 25 August): The Enterprise arrives at Deneva—the home of Captain Kirk's brother, Sam and his family—and discovers that the entire planet has been infested with large, amoeba-like aliens that have attacked and killed much of the Human population. One of these aliens attaches itself to Spock, who volunteers to become a subject in Dr. McCoy's medical tests. McCoy and Kirk rush to find a cure in time to save Spock and the remainder of the Denevan population.
- Reference Stardate 2/0808.26 (26 August): The U.S.S. Republic NCC-1371, under the command of Captain Richard V. Masterson, is officially listed as missing. Based on information obtained at the time, Starfleet officials believe that the vessel may have been missing as many as seven months prior.
- Stardate 3372.3 (approx. 25 September): An energy-based life form that feeds on negative emotions drives the crew of the Enterprise into brutal conflict with the Klingons.
- Stardate 3372.7 (approx. 26 September): When Mr. Spock begins to behave aggressively, Kirk discovers his first officer must return to Vulcan to take a mate, or he will die.
- Reference Stardate 2/0802: The brief war with the Klingon Empire, the imposed Organian Peace Treaty, and first contact with the Gorn have delayed the Federation Council's action on the Romulan border attack and the revelation of the genetic link between Vulcans and Romulans. Though Starfleet has doubled the number of patrols along the Romulan Neutral Zone and established new, larger, and more heavily armed border stations, no direct action against the Romulans is taken at this time.
- Stardate 3417.3 (approx. 12 October): Despite exposure to fatal radiation, the Federation colony on Omicron Ceti III appears to be thriving. A landing party from the Enterprise investigates, finding the colony's population to be healthy beyond explanation. Leila Kalomi, an old friend of Mr. Spock, shows the landing party strange flowers that seem to impose a state of pure bliss on all exposed to its spores, but at the cost of ambition and self-discipline.
- Stardate 3468.1 (approx. 30 October): The crew of the Enterprise are held captive by an alien who claims to be the Greek god Apollo.
- Reference Stardate 2/0911: Deep-cover Starfleet agents within the Klingon Empire report that the Klingons and the Romulan Star Empire have settled their border disputes and have likely sealed cease-fire agreements with military technology exchanges. In the resulting shake-up in Starfleet Intelligence, the entire staff of the Romulan Activities Unit is replaced. Federation Council members favoring a stronger stand against the Romulans feel that they have a mandate due to the strength of public opinion. As a result, they draft top-secret resolutions commissioning Operation Purloin.
- Stardate 3478.2 (approx. 3 November): Strange radiation exposes a landing party from the Enterprise to the effects of rapid aging.
- Stardate 3497.2 (approx. 10 November): The crew of the Enterprise becomes entangled in a planet's tribal power struggle.
- Stardate 3541.9 (approx. 26 November): The crew of the Enterprise deals with Nomad—an indestructible, planet-destroying space probe that thinks Kirk is its creator.
- Stardate 3614.9 (approx. 23 December): Mr. Scott is implicated in a series of bizarre murders.
- Stardate 3619.2 (approx. 25 December): Captain Kirk becomes obsessed with destroying an entity that killed many of the crew of his old ship.
Captain Kirk's five-year mission was established to have begun in 2265 in the Star Trek: Voyager episode "Q2". The Star Trek episode "The Menagerie, Part I" further establishes that Spock served under Captain Pike for 11 years, and that it had been 13 years since the events of "The Cage," meaning that Stardate 3012.4 fell two years into Kirk's command. The episode "Charlie X" further added weight to this, establishing both Stardate 1533.1 and the Earth date of Thanksgiving, which falls on 23 November in 2265. As the stardates ranged from the mid-1000s to the low 3000s in the first season and continued to increase at approximately 1000 per season afterward, it seems logical to conclude that the first season spanned nearly two years, and later seasons one each, with the second season chronicling the 3000s, the third season the 4000s and 5000s, and the Animated Series the 5000s. If Captain Kirk's command began on or about Stardate 1000, this would put the end of the five year mission on or about Stardate 6000, shortly after the end of the Animated Series. Using these dates as a reference point, the following can be established:
- Stardate 1000 fell on 13 May 2265.
- The range for Stardates each year is from X636 to Y635 (e.g., 1636 to 2635)
- This places "The Menagerie" (Stardate 3012.4) on 18 May 2267, at the beginning of Kirk's third year in command of the Enterprise
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