- Stardate 7636.2/Reference Stardate 2/1101: Starfleet Intelligence orders the Constitution class U.S.S. Hood NCC-1707, under the command of Captain Hugo Revere, to investigate the area of spatial interphase near Tholian space. The ship's assignment is to determine the potential of the interphase phenomenon as an offensive military weapon for Starfleet.
- Stardate 4657.5 (approx. 7 January): Kelvans from the Andromeda galaxy steal the Enterprise, modify it, and attempt to return home.
- Stardate Unknown: Captain Kirk must battle a deadly virus and a treacherous fellow starship captain to stop an intertribal war.
- Stardate Unknown: (VAN #7)
- Stardate 4729.4 (approx. 3 February): A new computer system causes havoc while being tested aboard the Enterprise.
- Stardate 4768.3 (approx. 17 February): Telepathic aliens take control of Kirk and Spock's bodies with the intention to build new, mechanized bodies for themselves.
- Stardate Unknown: During an historical research mission in 1968, the Enterprise encounters Gary Seven, a human with advanced technology who appears to be attempting to alter Earth's history.
- Stardate Unknown: (TOS: "From History's Shadow," Chapters 1, 2, 5, 9, 12, 16, 19, 22, 25, 27, 33, 37)
- Stardate 4842.6 (approx. 16 March): A mysterious alien device on a planet with a predominantly Native American culture erases Captain Kirk's memory, and he begins a life with them as a member of their tribe.
- Stardate 7662.4/Reference Stardate 2/1104: The Enterprise is ordered to assist and recover vital data from the Hood, which has become trapped in the interphase. The crew of the Enterprise is able to retrieve the needed information, but the Hood eventually disappears due to the interphase disturbance created by the presence of the Enterprise. Intelligence reports later verify that the interphase phenomenon is useless as a weapon.
- Stardate Unknown: (VAN #8)
- Reference Stardate 2/1105/Imperial Standard Date 448/3.4: The Constitution class cruiser U.S.S. Essex NCC-1697, under the command of Captain Salar, discovers a Klingon D-7 class cruiser, the I.K.S. Dun Da Spu', or "Great Book Strike," in the 34 Kraol system within the Triangle. A Klingon landing party is attempting to alter the cultural development of an intelligent race on the system's third planet, in order to tap the world's extensive durallium resources.
- Stardate 5027.3/Reference Stardate 2/1002: (approx. 22 May): The Enterprise participates in Operation Purloin, a Starfleet Intelligence operation to seize a prototype of a new Romulan cloaking device. The Enterprise escapes with both the device and confirmation of a Klingon/Romulan technological agreement. The device works once while escaping from the Romulan Neutral Zone, but later fails to function when detached from the Enterprise.
- Stardate 5029.5 (approx. 23 May): The crew of the Enterprise rescues a group of children stranded on a planet, along with their evil "imaginary" friend.
- Stardate 5121.5 (approx. 26 June): While visiting a doomed planet, an Enterprise landing party is subject to torturous experiments to test an empathic race.
- Reference Stardate 2/1004: Despite intense examination by the best minds in the Federation, the Romulan cloaking device remains a mystery. Nevertheless, political pressures force Starfleet to make a public demonstration of the stolen device. It is installed on a Federation ship, and dignitaries from all over the Federation fill both that ship and the vessel observing the experiment. When the cloaking device is activated, both ships disappear. Seconds later, there is a gigantic explosion, and neither ship ever reappears. Scientists stop all attempts to duplicate the cloaking device. Federation Council members who advocated a harder position against the Romulans, and who gained in stature because of the success of Operation Purloin, lose credibility because of the disaster.
- Reference Stardate 2/1109: Federation Genetics Research Station 17 (GRS 17), located on Aleph III near the Klingon Neutral Zone, is closed by Starfleet orders. The Enterprise is ordered to retrieve all personnel and data. Once there, the crew discovers Cyrano Jones, Tribbles, and a group of Klingons led by Commander Koloth.
- Stardate 5694.7 (approx. 29 September): (VAN #9, Chapter 3)
- Reference Stardate 2/1109.30 (30 September): An abandoned Romulan planetary base is discovered on Eridam, a mining world near the Triangle. Its Romulan inhabitants were wiped out by LV-132, a viral epidemic disease also known to affect Vulcans. No military information is gained, but personal diaries, children's books, works of fiction, and other non-military writings are recovered. This body of work, known as the Eridam Papers, adds much to the Federation's meager store of knowledge about the Romulans. The Vulcan connection is supported by anatomical drawings, Romulan legends, and children's history books. Based on the Eridam Papers, some political thinkers speculate that negotiation may be possible with the Empire. Others see no hope for negotiation and press for even stronger measures to curb "the Romulan threat." The Federation Council votes to maintain a stronger military presence along the Romulan Neutral Zone and near the Triangle, and asks Starfleet Intelligence to gather as much intelligence data as possible about Romulan military capabilities and tactics.
- Stardate 5423.4 (approx. 14 October): An overpopulated race of aliens abduct Kirk to solve their population problem.
- Stardate 5431.4 (approx. 17 October): Captain Kirk pursues aliens who have stolen Spock's brain.
- Stardate 5476.3 (approx. 2 November): As Dr. McCoy discovers he is dying of an incurable disease, the crew of the Enterprise rush to stop an asteroid from colliding with a Federation world, only to discover that the asteroid is, in fact, a disguised alien vessel. They find an entire civilization living in the ship who believe they are actually on a planet, and a dictatorial "Oracle" who forbids any attempt to discover the truth.
- Reference Stardate 2/1111: The U.S.S. Enterprise makes first contact with the I'lglii at Federation Deepspace Research Facility 39, where the I'lglii's presence disrupts research in transporter design. This intelligent, humanoid-sized amoeboid life form is capable of sublight travel without technological aid.
- Stardate 5630.7 (approx. 29 December): The Enterprise transports an alien ambassador who must travel inside a special case, because his appearance causes insanity.
- Stardate 5221.3: While exploring on the outermost rim of the galaxy, the Enterprise is pulled into the orbit of a dead star. Trapped there, the crew discovers that there is an ancient derelict pod ship trapped with them as well.
- Stardate 5373.4: Spock must travel to the past to rescue his younger self from danger.
- Stardate 5371.3: The Enterprise encounters a giant cloud creature that feeds on the energy of the planets that lie in its path. They determine it is heading for Mantilles, home to a Federation colony governed by former Starfleet officer Bob Wesley.
- Stardate 5143.3 (25 December): Patrolling near the Romulan Neutral Zone, the Enterprise finds a ship manned by Carter Winston, a Federation citizen and philanthropist who has been missing for five years.
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
The order given for the episodes of Star Trek: The Animated Series is taken from the novelizations, which included chronological references and additional story elements. While the novelizations gave new (and more consistent) stardates, the stardates given in the original episodes have been retained.
- McLimore, Guy W. Jr., Poehlein, Greg K., and Tepool, David F. "Ghosts of Conscience." Star Trek: The Role Playing Game, Book 2001B. Illustrations and Drawings by Mitch O'Connell and Jordan Weisman. FASA Corporation, 1983.
- Barton, William A., Gallagher, Tara J., Hess, Clare W. III, Huettel, Todd W., Kemper, Dale L., Menke, Bernard Edward, Pardoe, Blaine L., Peterson, Boy F., Rogan, Peter R., Stein, Kevin, Stuart, Rick David, and Theisen, John A. "Star Trek IV: The Voyage Home Sourcebook Update." Star Trek: The Role Playing Game, Supplement 2224. FASA Corporation. 1986.
- Roddenberry, Gene (Executive Producer). "By Any Other Name." Star Trek, Season 2, Episode 21. Directed by Marc Daniels. Story by Jerome Bixby Teleplay by Jerome Bixby & D.C. Fontana. Desilu Productions, 23 February 1968.
- Roddenberry, Gene (Executive Producer). "The Omega Glory." Star Trek, Season 2, Episode 25. Directed by Vincent McEveety. Written by Gene Roddenberry. Desilu Productions, 1 March 1968.
- Roddenberry, Gene (Executive Producer). "The Ultimate Computer." Star Trek, Season 2, Episode 24. Directed by John Meredyth Lucas. Story by Laurence N. Wolfe. Teleplay by D.C. Fontana. Desilu Productions, 8 March 1968.
- Roddenberry, Gene (Executive Producer). "Return to Tomorrow." Star Trek, Season 2, Episode 22. Directed by Ralph Senensky. Written by John Kingsbridge. Desilu Productions, 9 February 1968.
- Roddenberry, Gene (Executive Producer/Story). "Assignment: Earth." Star Trek, Season 2, Episode 26. Directed by Marc Daniels. Story by Gene Roddenberry & Art Wallace. Teleplay by Art Wallace. Desilu Productions, 29 March 1968.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "The Paradise Syndrome." Star Trek, Season 3, Episode 3. Directed by Jud Taylor. Written by Margaret Armen. Paramount Pictures Corporation, 4 October 1968.
- Michael Mornard. "An Imbalance of Power." Star Trek: The Role Playing Game, Supplement 2220. Illustrations by David R. Deitrick, Darnell Williams, and Jeff Laubenstein. FASA Corporation. 1986.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "The Enterprise Incident." Star Trek, Season 3, Episode 4. Directed by John Meredyth Lucas. Written by D.C. Fontana. Paramount Pictures Corporation, 27 September 1968.
- Wheeler, Wm. John with McLimore, Guy W. Jr., Poehlein, Greg K., and Tepool, David F. "Cadet's Orientation Sourcebook." Star Trek: The Role Playing Game, Book 2004A. FASA Corporation, 1983.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "And the Children Shall Lead." Star Trek, Season 3, Episode 5. Directed by Marvin Chomsky. Written by Edward J. Lakso. Paramount Pictures Corporation, 11 October 1968.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "The Empath." Star Trek, Season 3, Episode 8. Directed by John Erman. Written by Joyce Muskat. Paramount Pictures Corporation, 6 December 1968.
- McLimore, Guy W. Jr., Poehlein, Greg K., and Tepool, David F. "Again, Troublesome Tribbles." Star Trek: The Role Playing Game, Book 2001B. Illustrations and Drawings by Mitch O'Connell and Jordan Weisman. FASA Corporation, 1983.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "The Mark of Gideon." Star Trek, Season 3, Episode 17. Directed by Jud Taylor. Written by George F. Slavin and Stanley Adams. Paramount Pictures Corporation, 17 January 1969.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "Spock's Brain." Star Trek, Season 3, Episode 6. Directed by Marc Daniels. Written by Lee Cronin. Paramount Pictures Corporation, 20 September 1968.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "For the World is Hollow and I Have Touched the Sky." Star Trek, Season 3, Episode 10. Directed by Tony Leader. Written by Rik Vollaerts. Paramount Pictures Corporation, 8 November 1968.
- McLimore, Guy W. Jr. and Poehlein, Greg K. "The Vanished." Star Trek: The Role Playing Game, Supplement 2201. Illustrations by Mitchell O'Connell and Dana Andrews Knutson. FASA Corporation. 1983.
- Roddenberry, Gene (Executive Producer) and Freiberger, Fred (Producer). "Is There in Truth No Beauty?." Star Trek, Season 3, Episode 7. Directed by Ralph Senensky. Written by Jean Lisette Aroeste. Paramount Pictures Corporation, 18 October 1968.
- Scheimer, Lou & Prescott, Norm (Producers). "Beyond the Farthest Star." Star Trek: The Animated Series, Episode 4. Directed by Hal Sutherland. Written by Samuel A. Peeples. Filmation Associates, 8 September 1973.
- Scheimer, Lou & Prescott, Norm (Producers). "Yesteryear." Star Trek: The Animated Series, Episode 3. Directed by Hal Sutherland. Written by D.C. Fontana. Filmation Associates, 15 September 1973.
- Scheimer, Lou & Prescott, Norm (Producers). "One of Our Planets is Missing." Star Trek: The Animated Series, Episode 7. Directed by Hal Sutherland. Written by Marc Daniels. Filmation Associates, 22 September 1973.
- Scheimer, Lou & Prescott, Norm (Producers). "The Survivor." Star Trek: The Animated Series, Episode 5. Directed by Hal Sutherland. Written by James Schmerer. Filmation Associates, 13 October 1973.