In his book The Trouble with Tribbles, David Gerrold presents his case of failed story, outline or script submittals during his early attempts to write for Star Trek: The Original Series. These outlines were later presented in the same book.
"An Accident of Love"
"An Accident of Love" was a story assigned to writers Allan Balter and William Woodfield during the first season. However, the story assignment was cut off abruptly by the series production staff. (These Are the Voyages: TOS Season One, p. 361)
Step outline by Robert Barry, dated 22 May 1967. The story concerned a spaceship disguised as an asteroid. Although Barry's outline, according to the producers, was original and imaginative, it was deemed too expensive to produce. However, the concept was later reused in "For the World is Hollow and I Have Touched the Sky". (These Are the Voyages: TOS Season Two, p. 461)
Story outline by Norman Katkov, dated spring, 1966. Inspired by the 1958 sci-fi film It: The Terror from Beyond Space, the Enterprise is invaded by an invisible, powerful alien being, capable of smashing rooms and tossing crewmembers through the air. Roddenberry and his staff disliked the concept, deeming it too violent and too expensive. (These Are the Voyages: TOS Season One, p. 356)
This story dealt with an alien race kidnapping Kirk, Spock and McCoy in order to use their genes to create a gene bank, providing a way to survive for their infertile species. Meanwhile, they replace the trio with android duplicates on board the Enterprise. The crew soon begins to suspect their fellow officers to be imposters, as they behave oddly and unlike their real counterparts, and form a mutiny against them. (These Are the Voyages: TOS Season Three, p. 519)
Though Gerrold later speculated that Kirk would instead temporarily take command of another starship to investigate reports of laxity, his outline primarily set it aboard the Enterprise. Kirk discovers there's a mascot smuggled aboard by a crewmember; the creature, named Bandi, has an empathic ability to cause sympathy for it. Kirk wants it confined but Bandi always gets out by persuasive empathy to a crew member nearby. When a crewmember dies because of a distraction caused by Bandi, Kirk wants it off the ship; Bandi turns the crew against Kirk, but once Spock kills Bandi, the crew snaps out of it. This behavior by the crew led Gerrold to speculate Kirk temporarily commanding another ship where the problem happens. Gerrold also said if the outline sold, he'd come up with a better name than Bandi. Nevertheless, the name was later reused for "Encounter at Farpoint", the pilot episode of Star Trek: The Next Generation.
Daniels' outline had Kirk and three crewmembers in a shuttlecraft visiting a planet rich of "summium", a rare and precious mineral. However, the "summium" is guarded by "The Beast", a caretaker, who captures Kirk while the three crewmembers escape. When the Enterprise arrives, Kirk is beamed up, however, he still remains in the clutches of "The Beast". Finally, Anthropology Officer Janet Matthews, an Esper, is able to communicate with the creature, and convinces it to release the Captain.
Story outlines by David Gerrold, dated 14 March 1968 and 4 April 1968.   Additionally, in a period spanning from 12 March 1967 to 17 April 1968, there was material correspondence between Gerrold and Gene Roddenberry about this proposed episode.  The episode was intended to introduce the character of Bem. The reason why Gerrold named both that alien and this episode "Bem", an oft-used acronym for "Bug Eyed Monster," was simply because he thought it would be fun to have a true bug-eyed monster on Star Trek, even though the alien character was not intended to be one and (at least in Gerrold's opinion) there were never any bug-eyed monsters in the original Star Trek series. ("Bem" audio commentary)
The story's premise was related to prejudice, which was inspired by the push for civil rights that was occurring at the time, as many people were talking about the nature of prejudice. David Gerrold recalled, "People were saying that 'Prejudice isn't logical,' and I said, 'What would happen if you had a logical reason to be prejudiced?'"  Gerrold postulated the repercussions of having the very logical and emotionally-controlled Spock be the individual who became prejudiced. ("Bem" audio commentary) The question of what Spock might be prejudiced against, since there would have to be a logical reason for the reaction, then occurred to Gerrold. (; "Bem" audio commentary) The writer reckoned that having the character become prejudiced against an alien would be interesting.  Gerrold realized that the alien would have to be highly illogical and finally settled on the decision to make the alien a kind of practical joker. ("Bem" audio commentary; ) Gerrold concluded, "That was where 'Bem' started, with Spock having a logical reason to be prejudiced against Bem's bad behavior."  Gene Roddenberry granted Gerrold a contract to write the episode. (The Trek 25th Anniversary Celebration, p. 50)
The first of the story outlines involved the Enterprise struggling to courier a small team of scientists from a dismantling planet in the Zeta Omicron system to a position where they could observe their sun go nova. As well as Bem himself, this episode also featured the once-only character of Dr. Isaacson – the leader of the scientists and an absent-minded, glasses-wearing professor type. The outline included a reference to Christopher Pike and culminated in Spock, having been specifically targeted for Bem's practical jokes on the ship's crew, being irradiated by the nova (causing his skin to turn green with radiation burns) but Bem using his limbs, which could operate while detached from the rest of his body, to rescue Spock. In a tag set in sickbay, it was revealed that the reasoning for all of Bem's joke-playing on the crew was that Bem, unaware of the discomfort it had been causing Spock, had been expecting a practical joke to be played back on him, as a sign of acceptance. Spock had obliged, having given Bem a hot-foot. (The Trek 25th Anniversary Celebration, pp. 51-52)
The book The Trek 25th Anniversary Celebration (p. 51), in which an essay examines the details of the two story outlines, comments that the character of Dr. Isaacson was "obviously based" on Isaac Asimov.
David Gerrold admitted that this plot had problems, mainly centering around making Bem more responsible for the difficulties on the planet (rather than naturally-occurring problems due to the planet's break-up, such as earthquakes and storms) and writing Kirk as being more definite in the story's climax. Following the changeover of show-runner from Gene Roddenberry to Fred Freiberger, Gerrold was called in (by Freiberger) to rewrite "Bem". Roddenberry spoke to Gerrold about the story, and the narrative's writer liked some of Roddenberry's ideas. Wanting to take advantage of the opportunity, Gerrold compromised and agreed to write a revised version of the plot, in hopes of it satisfying both of them. (The Trek 25th Anniversary Celebration, p. 52)
The second version had Bem sabotaging a mission to determine whether the ape-like creatures of Zeta Beta II were civilized. It involved Bem trapping Kirk and Spock on the planet and fooling the rest of the Enterprise crew that the two senior officers were actually dead (as such, the outline included talk of the Enterprise returning to base, Kirk being buried on Earth and Spock on Vulcan). In this case, the episode's resolution involved Kirk and Spock (the natives having come to regard Kirk, because he showed them how to make tools, as a god) managing to capture Bem, a landing party from the Enterprise beaming to their location and Bem finally explaining that he was actually a psycho-sociologist who had been trying to conduct an experiment. In the outline's conclusion, Spock wondered – back aboard the Enterprise, as the ship departed the planet – whether the natives would use the concept of tools to construct tools or weapons and the creatures confirming, for the reader, that the former was true. (The Trek 25th Anniversary Celebration, pp. 52-54)
Fred Freiberger was still unhappy with the narrative. (The Trek 25th Anniversary Celebration, p. 54) Even though David Gerrold had submitted (together with the original outline) some sketches for the design of Bem's species, Gerrold later remembered, "We never got there because Gene left the show and Freddy Freiberger came in [....] I had the [revised] idea for 'Bem', but he said, 'I don't like that, either.'"  Gerrold elaborated, "There were more important stories to tell [....] Even though Gene was interested in it, for the third season of Star Trek, when he left and Fred Freiberger came in, there was a different storytelling agenda on the map." ("Bem" audio commentary) Dorothy Fontana said of the story, "We thought it could not be done well in live action." (Star Trek: The Magazine Volume 1, Issue 16, p. 67) She clarified, "It was impossible to do, in terms of production, at that time." (Star Trek Vault: 40 Years From The Archives, p. 32) The story outlines ended up in David Gerrold's possession and, at one point, he was storing them in his garage.  Although never developed for TOS, the episode (along with "More Tribbles, More Troubles", another story that David Gerrold unsuccessfully suggested for TOS) was ultimately developed for Star Trek: The Animated Series (for more information, see "Bem").
"Beware of Gryptons Bearing Gifts"
Story outline by David P. Harmon, dated 16 April 1968. This story featured the Enterprise being shrunk down to miniature size and placed on a tabletop (similarly to "Requiem for Methuselah") by a strange alien race. The producers didn't see much point in the story, and also deemed the notion of crewmembers being chased by a giant cat to be a rip-off from "Catspaw", and shut it off in an early stage. (These Are the Voyages: TOS Season Three)
"Chicago II", also known as "The Syndicate" was a story outline by George Clayton Johnson, based on Gene Roddenberry's idea "President Capone" in his original series proposal, "Star Trek is...", dealing with a parallel development planet where the gangster mobs took over and rule society.
Johnson's story didn't quite work out, and Roddenberry assigned him to work on "The Man Trap" instead. Later, in the second season, Gene Coon and David P. Harmon resurrected the story idea and turned it into a comedy, titled "Mission Into Chaos" and later, "A Piece of the Action". (These Are the Voyages: TOS Season One, p. 356)
"Dead Man's Shoes"
"Dead Man's Shoes" would have been about a planet of assassins. (Star Trek Monthly issue 26, p. 28)
"The Deadliest Game"
"The Deadliest Game" was once described by Robert Justman as "playing aboard the Mary Celeste on a quest for the treasure of Sierra Madre, which is a fountain of youth located on a hell planet!" (Star Trek Monthly issue 26, p. 28)
Following "Mudd's Women" and "I, Mudd", a third TOS episode featuring the character of Harry Mudd was originally planned. Titled "Deep Mudd", the story was written by regular Mudd writer Stephen Kandel. (Starlog Issue #117, p. 44; The Star Trek Interview Book, pp. 133 & 134)
The plot was conceived as a direct sequel to "I, Mudd", following Harry Mudd's entrapment on Planet Mudd, amid the androids there. "'Deep Mudd' involves Mudd's escape from that world, after he tricked these particular robots into revealing to him the location of a cache of scientific equipment and weaponry left by their makers," explained Kandel. "Suddenly Mudd found himself with very, very advanced armament, which he used to bribe a group of pirates into helping him escape. The problem was, of course, that he could control neither the weapons nor the real heavies he was supposed to be in control of, the pirates. They tangled with the Enterprise, on a planet with a surface of molten, viscous mud. And it went on from there. That was basically it: bailing Harry Mudd out of his own problems, getting control of this weaponry they couldn't destroy, and sending it into a sun." (The Star Trek Interview Book, pp. 133-134)
The episode could not go ahead because Mudd actor Roger C. Carmel was unavailable at the time, busily involved with a film. (Starlog Issue #117, p. 44) Also, Gene Roddenberry was against doing "pirate stories". (These Are the Voyages: TOS Season Two, p. 283) The story ended up in Kandel's possession who, in a 1988 interview, remarked, "I still have the story somewhere." (The Star Trek Interview Book, p. 133)
Undated story outline by science fiction writer Hank Stine.
Undated story outline by Charles Parker.
"The Foreseeable Future"
Story outlines by Jean Lisette Aroeste, dated 22 August 1968 and 16 September 1968. The story revolved around a race of telepaths with precognition abilities, who were able to see their own near future. One of the telepaths, a young woman, had a vision concerning Captain Kirk, telling him he's going to die if he leaves the planet. The main theme of the story was accepting our fate as inevitable and letting it happen, or trying to change the outcome instead. The producers were not impressed with Aroeste's outlines, leading her to abandon this idea and come up with another story instead, titled "A Handful of Dust" (filmed as "All Our Yesterdays"). (These Are the Voyages: TOS Season Three, p. 519)
"From the First Day to the Last"
Shelved envelope for "The Menagerie" by John D.F. Black, delivered 8/12/1966
"Galatea of Polydor"
The Enterprise escorts a diplomatic team from the planet Polydor, among them a woman named Galatea, who bears an uncanny resemblance to one of Kirk's old lovers. Unbeknownst to the crew, the diplomats are actually humanoid robots. However, the transporter has somehow changed the androids, who now want to be free and lead their own lives, at all costs.
The production staff deemed the story to be unexciting, and chose not to develop it further. A similar story premise was successfully pitched later by Jerome Bixby, which became "Requiem for Methuselah". (These Are the Voyages: TOS Season Three, pp. 9-10)
The story was about an alien race who created a way to accumulate their vast knowledge, placing it in the mind of one selected individual. However, this person (the titular "Godhead") became too powerful and delusional by all this, and decided to take over the Enterprise with the intent on conquering the galaxy. The story was developed further and selected by Fred Freiberger to be filmed as the 26th episode of the third season. However, NBC canceled the series without ordering the last two episodes, resulting in "The Godhead" never being produced. (These Are the Voyages: TOS Season Three)
"Happy Birthday to You"
"Happy Birthday to You" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28)
"He Walked Among Us"
"He Walked Among Us" was a script written by Gene L. Coon and Norman Spinrad for TOS Season 2. Story outlines were dated 12 May 1967, 17 May 1967, and 18 May 1967. The first draft was dated 25 July 1967, and a later draft dated 28 September 1967.
The producers approached Spinrad with the task to write an episode to be a vehicle for Milton Berle, who expressed interest in appearing on Star Trek. Also, since a tribal village set was available, they told him to write a story in which it could be used.
The original story by Spinrad was about a primitive race called the Jugali, inexplicably employing technology well beyond their capacities, as a result of interference by Byrne, a Federation sociologist, who only wanted to do good, but it eventually resulted in terrible consequences.
However, Producer Gene L. Coon rewrote the episode to become a comedy. The rewritten story involved a Federation health food nut taking over a planet, so flagrantly breaking the Prime Directive that Kirk can't ignore him. He has set himself up as a god, refuses to depart from the planet when asked to and has so tightly woven himself into the planet's society that Kirk is unable to force him to leave without completely disrupting the society himself.
Unhappy with the result, Spinrad asked Gene Roddenberry to discard it, and "don't embarrass his show by shooting this piece of ----." He told Roddenberry to "read it and weep." Roddenberry agreed, and the episode was not produced. (Star Trek Monthly issue 26, p. 24)  
This story outline, dated 21 March 1966, sees a temporal experiment result in a 19th century man known as Alois Schicklgruber accidentally beamed aboard the Enterprise, with the crew entertaining and befriending him as they work on a way to return him to his own time. Soon, however, the crew realizes that in later life, he will change his name to "Alois Hitler" and have a son known as Adolf Hitler. This results in a dispute among the crew, with a Jewish geneticist advocating that the crew forcibly sterilize Schicklgruber so as to prevent the birth of his infamous son, but the Enterprise historian arguing that he cannot be blamed for the crimes of his son, especially seeing how he died when Adolf was only 13 years old.
No writer is credited on the outline, though given that it appears as part of Gene Roddenberry's archive, he may have been the author. The story does not appear to have progressed beyond its initial outline. 
"Image of the Beast"
Story outline by science fiction writer Philip José Farmer, dated 27 March 1966. In this story, the Enterprise discovers the wreck of an immense alien space ship crash-landed on a desert planet. The crew search the ghost vessel, and begin to experience memory losses and strange hallucinations. We learn that during a blackout, they had devices implanted into their skulls, allowing the telepathic aliens to communicate with them.
The story was deemed both too expensive to produce and too cerebral for NBC by the production staff. (These Are the Voyages: TOS Season One, p. 362) Farmer subsequently published the dark erotic science fiction/horror novel also entitled Image of the Beast, which had nothing to do with his Star Trek proposal except for the title.
"Japan Triumphs" was a story outline assigned to Gene Coon by Gene Roddenberry in March 1968 to be developed for the third season. Supposedly, it revolved around Japan winning World War II, thus creating an alternate timeline. However, it was abandoned by new producer Fred Freiberger, as Coon was too busy producing It Takes a Thief. (These Are the Voyages: TOS Season Three, p. 516)
"Joanna" was written by Dorothy Fontana as the first episode to feature Joanna McCoy, the daughter of Leonard McCoy. The outline was submitted 27 August 1968 and was later heavily rewritten to become "The Way to Eden".  The original story featured Joanna coming aboard the Enterprise and having a romantic fling with Kirk, causing major conflict between Dr. McCoy and Kirk, and Dr. McCoy and his daughter. 
"Journey To Reolite"
Story outline by Alfred Brenner, dated 18 April 1966. The Enterprise is transporting the leader of the planet Acrid for peace talks to their neighboring world Reolite. The Acrids are harsh and militaristic, while the Reolites are peace-loving democratic humanist. The Acrid leader and his mistress, Galatea, carry a rare "life-giving drug" as a gift to the Reolites, which also works as an aphrodisiac. Although it went unproduced, this outline served as a basis for the third season episode "Elaan of Troyius". (These Are the Voyages: TOS Season One, p. 356)
"The Joy Machine"
Story outlines by Theodore Sturgeon, dated 16 May 1967 and 23 June 1967. First draft teleplay by Meyer Dolinsky dated 21 October 1968. This script was later novelized under the same title, The Joy Machine, by James Gunn in 1996.
Sturgeon's story (first titled "The Root of Evil"), originally submitted for the second season, dealt with the population of a Federation colony getting addicted to a sophisticated machine stimulating the brain's pleasure center, which rewarded the workers with "hours of joy" in exchange for the work hours. Sturgeon's story was highly cerebral, and lacked any action-adventure, yet Robert Justman pushed for developing it further. In the next rewrite, now adding more jeopardy, Spock becomes addicted to the machine too.
Fred Freiberger resurrected the concept for the third season, and assigned Meyer Dolinsky to develop it into a workable screenplay. Dolinsky reworked the story, which now took place on a planet inhabited by mentally ill people, and featured a love story for Scotty. The machine now threatened the entire crew of the Enterprise, and made both McCoy and Scotty its slaves.
"The Joy Machine" was set to be produced as the 25th episode of the season, and the directorial debut of William Shatner. However, NBC cancelled the series after only 24 episodes of the third season, thus making "Turnabout Intruder" the last episode produced. (These Are the Voyages: TOS Season Three)
"The Judgment" was an unsolicited script submission by Ric Touceda, which was delivered to the Star Trek staff on 5 February 1968. Robert Justman claimed that the premise is good and the story is mysterious, romantic and intriguing. However, they "can't take the time or effort to train [Touceda] in the gentle art of writing for television". Roddenberry deemed that the story is "not worth buying, even as a bare idea". A year later, Touceda managed to sell a script to The Beverly Hillbillies. (These Are the Voyages: TOS Season Three, pp. 11-12)
"Kathi" was an unsolicited script submitted by then-novice writer Jean Lorrah early in the third season. Robert Justman read the script, but turned it down, claiming "there is nothing in the story that we have not dealt with before on Star Trek.", and that the structure gets confusing, and the work is often very boring. The story centered around a real person and a robot copy. (These Are the Voyages: TOS Season Three, p. 12)
"The Land of Counter-Pain"
"The Land of Counter-Pain" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28) It was submitted as an unsolicited script around the beginning of the third season by a non-professional writer identified as "Jill S.". The teleplay was read by Robert Justman, who turned it down, claiming that it was beautifully written, yet completely unsuitable for a television budget and Star Trek's action-adventure format. (These Are the Voyages: TOS Season Three, pp. 12-13)
"Lord, How Others Seem to Care"
This story was submitted by Morris Chapnick, who served as Desilu executive Herb Solow's assistant in the previous two years, in early-March 1968. The basic premise was what happens to a man who has been active throughout his whole life, and then finds himself cast aside and useless at the termination of his career. Roddenberry and Robert Justman found the story well-written, yet not what they were looking for at the moment, and turned it down. (These Are the Voyages: TOS Season Three, p. 14)
"The Lost Star"
This was Lucas' second writing assignment on the series after "The Changeling". The story revolved around a solar system located inside a powerful force field, hiding it from visitors. While penetrating the force field, the Enterprise gets severly damaged. Kirk leads a landing party to the nearby planet to find the materials needed to repair the ship, and discovers a race of primitive Humans, allegedly kept as slaves by a race called the "Old Ones", living in a modern city. Eventually, through Spock's mind meld with Kollos, a female in training to become one of the leaders, it is revealed that the "Old Ones" have perished centuries before by a genocidal war they brought on themselves, and the force field was created to camouflage their solar system in order to prevent the surviving natives from harmful outside intervention. Only a few selected leaders are aware of the technological advancements left behind by their ancestors. Through the mind link, Spock convinces Kollos that the Enterprise crew and the Federation does not represent harm, and eventually – after repairs are completed – the ship is set free by Kollos creating a "tunnel in space" through the force field. The crew (and the viewers) are left to wonder if Kollos will incite changes on her world or be killed by those who fear it.
Stan Robertson rejected the outlines, saying that though they're "well written", they're "lacking excitement, color and emotional involvement". Lucas went on to write "Patterns of Force" instead. (These Are the Voyages: TOS Season Two, pp. 466-467)
"Machines Are Better"
In this story, the Enterprise discovers a desolated planet with only two survivors: a pair of androids named Number One and Number Two, with an apparent feud against each other. Beamed aboard the ship, the two androids continue their competing, and eventually Number One – who moves faster than light – takes over control of the Enterprise.
Although more developed than van Vogt's previous submission, this story was still mostly unsuitable for television, and resembled another story involving androids, "I, Mudd". It was eventually turned down by Stan Robertson, who favored "I, Mudd" over it, and the story was scrapped. (These Are the Voyages: TOS Season Two, pp. 458-460)
"The Machine That Went too Far"
"The Machine That Went too Far" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 29) The story outline by A.E. van Vogt and Jack Williamson was delivered on 5 April 1966, and a revised version was delivered by the same writers on 20 April 1966. Story cut-off was exercised on 27 April 1966.
"The Magicks of Megas-Tu"
According to Larry Brody's book Turning Points in Television (p. 129), one particular story was written by him in 1969 for the third season of TOS – as he had been disappointed with previous installments of that season – and was sent to NBC by Brody's agent at the time, Sylvia Hirsch. In the book, Brody cryptically refers to third season producer Fred Freiberger as "Howie Horowitz" (perhaps confusing him with Howie Horwitz, producer of the 1960s Batman and 77 Sunset Strip as well as the Gene Roddenberry pilot The Questor Tapes) and relates about the plot idea, "The subject matter was as true to me as the egotism of thinking I could show Howie H. how the show should be [....] Howie Horowitz passed on buying the script, and on meeting with me." Three years later in 1972, Brody successfully pitched the same story, which involved the Enterprise encountering God in space, to Gene Roddenberry for the animated Star Trek series (for more information, see "The Magicks of Megas-Tu").
Story outline by Philip José Farmer, dated 26 March 1966. The Enterprise rescues a woman from a wrecked ship, who falls in love with Kirk. Lovesick over his refusal of her, she arms herself with a phaser and takes over engineering, setting the ship hurling through space at never before seen speeds. This causes the Enterprise to break through into a space void and get trapped inside.
The story was deemed too expensive to produce, however, elements from it apparently (coincidentally or not) resurfaced in "Is There in Truth No Beauty?". (These Are the Voyages: TOS Season One, pp. 361-362)
A woman believing herself to be in a relationship with the captain, then taking over engineering and sending the ship hurtling out of control, is also central to the plot of Farmer's novella "The Shadow of Space" (Worlds of If, November 1967); see entry under that title below.
Story pitch by John Kneubuhl, which never made it further, due to the problems with Kneubuhl during development of his previous story, "Bread and Circuses". (These Are the Voyages: TOS Season Two, p. 466)
"Miss Gulliver" by A.E. van Vogt was to have been about a woman who grew to gigantic proportions due to an accident related to an unsuccessful experiment in regrowing limbs. At the episode's conclusion, her lover also underwent the experiment, so that he too could undergo massive growth, and the couple were left to found a planet of giants. (Star Trek Monthly issue 26, p. 29)
Robert Justman commented that it "bears a striking resemblance to "Who Mourns for Adonais?" – namely that someone grows larger and larger and larger. After that, it bears no resemblance to anything whatsoever that we would be able to depict on film…" (These Are the Voyages: TOS Season Two, p. 459)
"Mission Into Chaos"
"More Tribbles, More Troubles"
Meant as a sequel to "The Trouble with Tribbles", "More Tribbles, More Troubles" began development as an episode for the third season of TOS, intended to be the first aired installment of that season. (The Trek 25th Anniversary Celebration, p. 50; )
After Fred Freiberger (the producer of TOS Season 3) watched "The Trouble with Tribbles" on the morning before he first met David Gerrold and decided that he hated the episode's comedic tone, Gerrold consequently realized that Freiberger – who had essentially replaced Gene Roddenberry as showrunner – would not want a tribble-related sequel. (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 97; episode audio commentary) Gerrold recalled, "I knew right then that – even though Gene had promised we were gonna do another tribble episode, in Star Trek's third season – I knew that it was dead." (episode audio commentary) Additionally, Gerrold remembered, "I said, 'Well, Gene said he wanted a sequel,' and [Freddy Freiberger] said that he had no interest." (Captains' Logs Supplemental - The Unauthorized Guide to the New Trek Voyages, p. 97) Gerrold concluded, "He killed the second tribble episode for the third season." 
Together with David Gerrold's "Bem", this tribble-centric installment was one of two episode ideas that, despite never undergoing development for TOS, were successfully resurrected for Star Trek: The Animated Series (for more information, see "More Tribbles, More Troubles"). Following the first broadcast of the episode's animated form, an adolescent, male Star Trek fan accused Gerrold of having plagiarized his idea for a tribbles-related sequel but Gene Roddenberry – in the knowledge that Gerrold had pitched the episode idea for the third season of TOS – simply asked Gerrold to "please handle" it. A reply letter that the writer sent to his accuser included the fact that he had planned the original tribble sequel for TOS' third season. ("More Tribbles, More Troubles" audio commentary)
Undated draft by Jerome Bixby. (citation needed • edit) The script of "Mother Tiger" was written by Bixby in about four days. He later remembered the plot; "It was [...] about an alien in space in suspended animation. Her race had long since perished, but they had sent her forth as a racial mother, hoping she would be resuscitated on some planet, and restore her race. The Enterprise picks her up, and ends up leaving her on a planet after she creates all kinds of mischief aboard ship; she's very powerful and intelligent."
The reason "Mother Tiger" wasn't produced was that doing so was considered too expensive. Nonetheless, the script had several aftereffects and was very well received by the TOS creative staff. Recalled Jerome Bixby, "They flipped over it, but said, 'We don't usually put $7 million into a Star Trek episode' [....] While they couldn't use it, they said I had an uncunny feel for the show and made me one of their regulars [....] Several later episodes seemed to reflect elements of ['Mother Tiger'], namely '"The Devil in the Dark", with a racial mother, the rock creature." (Starlog, issue #164, p. 48)
"One Million B.C."
"One Million B.C." was a story outline assigned to Gene Coon by Gene Roddenberry in March 1968 to be developed for the third season. However, it was abandoned by new producer Fred Freiberger, as Coon was too busy producing It Takes a Thief. (These Are the Voyages: TOS Season Three, p. 516)
"The Orchid People"
Story outline by Catherine Turney and John Collier, dated 3 April 1967. In this story, the Enterprise receives a distress call from an unexplored planet. Despite objections by Spock, Kirk decides to investigate the matter, and finds two exceptionally beautiful men and an exceptionally beautiful woman on the planet surface. Beamed aboard the Enterprise, the three aliens turn out to be irresistable to anyone they turn their charms towards. The two males try to seduce the female crewmembers, while the female tries to lure Kirk. It turns out the aliens feed on the "life energy" of those they seduce, and that's how their race died out, by the stronger one nourishing the energy of the weaker. The three survivors made a pact never to use their fatal powers against each other, as they now have plenty of "food supply" among the Enterprise crew.
Despite the story being deemed similar to "The Man Trap", the production staff liked the concept, and hence they bought the story rights. However, as Turney and Collier relocated to Europe, logistics and time conflicts prevented it to be developed further. (These Are the Voyages: TOS Season Two, pp. 457-458) The story is similar to TAS: "The Lorelei Signal", TNG: "Man of the People" and VOY: "Favorite Son".
Story outlines by Daniel Louis Aubry, dated 8 August 1967 and 9 September 1967. This story dealt with the Enterprise discovering sentient rock creatures living on an asteroid intended to be used as a Federation outpost. The creatures feed on plutonium, and kill a couple of Enterprise crewmembers while attempting to eat from the portable nuclear generators brought to the asteroid. Kirk devises a plan to destroy the creatures, however, Spock discovers that when gorged, they emit an energy which can be harnessed to great use, and convinces the Captain to try communicating with them.
Apart from being an apparent rip-off from "The Devil in the Dark", these outlines had many flaws, and the production staff quickly and unanimously decided to scrap the story. (These Are the Voyages: TOS Season Two, pp. 469-470)
"The Pastel Terror"
"Perchance to Dream"
"Portrait in Black and White"
Based on Gene Roddenberry's story concept "Kongo" in his 1964 series proposal Star Trek is..., this story dealt with a parallel development planet, where the "Ole Plantation Days" were occuring, with reversed roles of blacks and whites, with the white savages being shipped off and sold on slave markets operated by black traders.
Stephen Kandel described the story as "a show with a very militaristic planet being discovered, and the inhabitants were black. The only one they would talk to was Uhura, and they regarded the others as nothing." (Starlog Issue #117, p. 44)
In The World of Star Trek, David Gerrold revealed that DeForest Kelley had always wanted to see this story, featuring himself and Nichelle Nichols, described as "something where the two of us were thrown onto a planet where there was a great racial problem, only reversed. The fact that I am a Southerner and she is black, and that we're trapped on this planet together."
Despite Robert Justman's heavy objections about the story being too violent, and several aspects (such as a "breeding farm" of white slaves) being unacceptable to television censors, Roddenberry was very fond of this story, seeing it as a perfect example of the "Gulliver's Travels" concept he originally envisioned Star Trek to be, and pushed for it being developed further.
The story was submitted to NBC. However, program manager Stan Robertson rejected it in a short and stiff letter, saying, "We believe that this story does not fit into the Star Trek concept." Despite the rejection, Roddenberry still pushed for the story to be developed, ready to fight the network if necessary, and it went through re-writes by Gene Coon, Steven W. Carabatsos and D.C. Fontana. However, due to the lack of network support and the writers never being able to develop it into a workable form, the story was never produced. (These Are the Voyages: TOS Season One, pp. 358-360)
According to Gerrold, "A script version had even been written. And rewritten. And rewritten. (…) But either the premise was too touchy for television or nobody could quite make it work. The script never reached a form where Roddenberry or Coon wanted to put it into production."
Stephen Kandel referred to the fact that the story was not given the go-ahead as "unfortunate" and went on to say, "I would love to have done it." (Starlog Issue #117, p. 44)
Although the reference book Inside Star Trek: The Real Story (pp. 197 & 399) attests that this story developed into "Let That Be Your Last Battlefield", documentation from the series' production disproves this and confirms that "Portrait in Black and White" was ultimately never developed. (Gene Roddenberry Collection, UCLA)
"The Protracted Man"
Although warp drive allows speedy travel, it still involves travel over immense distances; Starfleet is participating in a test of a space warp corridor that will take seconds to cross several light years. The Enterprise will wait at the exit point to recover the shuttlecraft being piloted through. However, something goes wrong, the shuttle can't exit, and the pilot is beamed out from within the warp corridor. The pilot, however, is protracted: three visual representations – each of a different color (e.g. blue, red, yellow) – move a fraction of a second apart when the man is moving; his voice is similarly garbled by a separation in time; the pilot is drawing energy from the Enterprise to maintain himself. The protraction keeps increasing, particularly when the ship tries to move at warp speed to get to a point in space where all power can be shut down briefly to try to restore the pilot to normal. The transporter is used to reintegrate the man by dematerializing the multiple images then overlaying them.
Gerrold was inspired by a "protraction"-type sequence in the film West Side Story (which was directed by Robert Wise), wondering what the effect would suggest, then writing the script outline. In the movie, the teens go to a dance, with the teens appearing in a similar way, though the walls of buildings stay solid and grim-looking, by combining the film colors out of synchronization.
"The Rebels Unthawed"
"The Rebels Unthawed" was a story outline written by Philip José Farmer. The Enterprise and its crew encounter a derelict space ship, abandoned and floating in space. Inside the craft, they find twelve passengers who are frozen in suspended animation. Once they are revived, it is revealed they were abducted from Earth by aliens, during the American Civil War. Adjusting to the future time period in which they have been awoken turns out to be considerably difficult for the newcomers. The outline was rejected because it resembled too much to "Space Seed", another story already in development. Farmer later wrote the Star Trek story treatment into a short story.  (These Are the Voyages: TOS Season One, p. 362) This story also bears a resemblance to VOY: "The 37's".
"Return to Eden"
Story outlines by Alvin Boretz, dated 9 May 1966 and 23 May 1966. The Enterprise comes across a planet with automated people, where everything is "perfected": no crime, no hunger, no illness, no choice. But the society is completely sterile and the people are automated zombies of a computerized society. Robert Justman thought the story was awful. (These Are the Voyages: TOS Season One, p. 357) This story also highly resembles Roddenberry's "The Return of the Archons", which was probably another reason why it was not purchased.
"Rites of Fertility"
Story outline by Robert Sheckley, dated 6 May 1966. An Enterprise crewman becomes infected with a strange "disease". His skin hardens, his nails grow into leaves and he transforms into a living, thinking vegetable. The transformation soon affects the entire crew, except for Spock, who has an immunity. In search of a cure, Spock beams down to a nearby planet inhabited by a primitive Indian-like race, who worships trees and longs to one day become one with their gods. They are reluctant to share the cure until Spock explains to them that Earth people do not consider turning into a plant an acceptable form of immortality.
The potential costs of Sheckley's outline were deemed to be far beyond the budget of a weekly television series, hence it went unproduced. (These Are the Voyages: TOS Season One, p. 357)
"Rock-A-Bye Baby, Or Die!"
Story outline by George Clayton Johnson, dated 2 August 1966, concerning a newborn interstellar entity coming to life, aging, and dying within the Enterprise's computer and circuitry. The outline is collected in a hardcover omnibus of Johnson's writings, All of Us Are Dying and Other Stories, published by Subterranean Press in 1999.  A similar premise was the basis for TNG: "Emergence".
"The Search For Eternity"
Story outline by A.E. van Vogt, dated 11 April 1967. In the story, the Enterprise crew awakens to find themselves unable to remember the past few hours. It turns out that during this time, Kirk apparently ordered the destruction of a populated planet, whose inhabitants now blame him with genocide. Recordings of the destruction and a missing photon torpedo appear to justify the claim. A Federation Admiral then arrives on his own starship, and orders Kirk to be executed by firing squad. It turns out all is, in reality, a ploy devised by a reptilian-looking species who have faked the attack and can pose as Starfleet members (including the Admiral), in order to gain control of the Enterprise and wage war on the Federation. The story bears a resemblance to TNG: "Conundrum" and ENT: "Shockwave". The aspect of a photon torpedo being unaccounted for after an alleged act of instigation by the Enterprise resembles, albeit most likely coincidentally, part of the plot of Star Trek VI: The Undiscovered Country.
"The Shadow of Space"
"The Shadow of Space" was written by Philip José Farmer in 1966.  The Enterprise travels outside the universe. Farmer published a prose adaptation of the idea, under the same title, but with names and background changed from Star Trek for copyright reasons. The story first appeared in the science fiction magazine Worlds of If and subsequently in a collection of Farmer's short fiction.
Story outlines by Darlene Hartman, dated 24 June 1967, 15 July 1967, and 24 July 1967. First draft teleplay dated 23 August 1967. Hartman's story dealt with the Enterprise finding a primitive civilization living in a Garden of Eden environment under the control of a giant computer named Shol, which the natives consider to be a god. When Shol begins to "absorb" the Enterprise crewmembers into itself, Kirk and Spock are forced to destroy it. The natives are now left without their "god" and have to accept their loneliness from then on.
This story went through several revisions, mostly because Gene Coon saw a potential talent in Hartman, and because both Coon and Gene Roddenberry thought it had a strong poetic quality. However, when Max Ehrlich's similar story, "The Apple" went into production, "Shol" was shelved. Coon still wanted to develop the story further, eventually assigning Hartman to write a teleplay, but after Coon's departure from the series the new producer John Meredyth Lucas ultimately scrapped it. (These Are the Voyages: TOS Season Two) The character of Dr. M'Benga, however, who was introduced in this story, remained with the series and appeared in other episodes.
"Shore Leave II"
Story outline by Theodore Sturgeon, dated 24 April 1968. The sequel to "Shore Leave" was assigned by Roddenberry to Sturgeon in March 1968. However, as Sturgeon already proved (with "Shore Leave", "Amok Time", and the unproduced "The Joy Machine") to write his scripts very slowly and having no real knowledge of writing television drama, and Roddenberry had enough of "baby-sitting writers" at that point, the assignment was eventually cut off at outline stage. (These Are the Voyages: TOS Season Three, p. 516)
"Sister In Space"
Story outline by Robert Sheckley, dated 14 June 1966. Sheckley's second attempt after the failed "Rites of Fertility" outline had the Enterprise discover a long-lost Starfleet vessel, the USS Yorktown dead in space. Kirk, Scotty, Sulu, Rand and a few "redshirts" beam aboard and discover that an unknown and lethal alien creature killed the Yorktown crew. The creature attacks one of the "redshirts", and rips him limb from limb. Aside its enormous strength, the alien monster is also a chameleon capable of blending into the background.
The outline, which almost gave Robert Justman a heart attack, was deemed much too expensive to be produced within Star Trek's budget, so Sheckley was turned down once again. (These Are the Voyages: TOS Season One, pp. 357-358) The story seems broadly similar to the later Alien and Predator film franchises.
Undated outline by Jerome Bixby.
"Sketches Among The Ruins of My Mind"
"Sketches Among The Ruins of My Mind" was written by Philip José Farmer in 1966. As with his previous "The Shadow of Space", Farmer later used the idea as the basis of a published novella, though in this case he removed all vestiges of its Star Trek origin. According to Farmer, Roddenberry found the idea too sophisticated for a general audience. In the novella, an alien satellite enters Earth orbit and wipes (or records) everyone's most recent 4 days' worth of memories once each 24-hour day; a person would lose the last 28 days' memories by the end of the first week, etc.
Undated outline by Robert Bloch. Bloch's second story after "What Are Little Girls Made Of?" dealt with a 21st century gangster who puts himself into suspended animation to avoid being prosecuted for his crimes, found by the Enterprise centuries later. Gene Coon immediately nixed the idea, as it resembled too much to "Space Seed", a story already in development. (These Are the Voyages: TOS Season One, p. 362)
"Spirit of the Enterprise"
"Spirit of the Enterprise" was an unsolicited script submitted by Theodore Sturgeon in behalf of a friend, in November 1967. It dealt with another starship crash-landed into the ocean of a planet, discovered by the Enterprise. Eventually, "ghosts" of the ill-fated crew begin haunting the Enterprise corridors. Both story editor D.C. Fontana and producer John Meredyth Lucas disliked the story – the former claiming it would suit Voyage to the Bottom of the Sea better – and turned it down. (These Are the Voyages: TOS Season Three, pp. 10-11)
Spock's leg story
At one point, Gene Roddenberry planned to do an episode set before the original Star Trek pilot, "The Cage", in which Spock would have injured one of his legs. As a way to set the story up, Roddenberry asked Leonard Nimoy to limp during "The Cage", an instruction with which Nimoy complied. "But we never did an episode on Spock's leg!" Nimoy stated at 2001 Slanted Fedora convention in Las Vegas, where Nimoy also revealed the origins of Spock's limp in "The Cage".
"The Squaw" was written by Wincelberg as a "compensation" by Roddenberry for rewriting his script for "Dagger of the Mind". (He also got to work on "The Galileo Seven" for the same reason.) The story featured a lost colony of Humans who have based their society on the tropes contained in a third-rate pulp Western novel left behind by their ancestors. The planet is also inhabited by lost Vulcans, who live in a primitive tribal state and aggress against the Humans. The Vulcans, it turns out, were peaceful, until the Humans arrived and began to harass and hunt them, like the Old West characters did with the Indians in the book. (These Are the Voyages: TOS Season One, p. 361)
A number of the script's elements would resurface in later Star Trek productions. A book mistakenly serving as the basis for a civilization appeared in "A Piece of the Action", in another way, TNG: "The Royale". A very similar story premise was produced almost forty years later, as ENT: "North Star".
"The Surrender of Planet X"
Undated outline by Don Masselink.
"The Takeover" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28)
"That Infernal Machine"
"That Infernal Machine" was an unsolicited full teleplay submitted by a fan identified as "Joyce V." in early March 1968. The story had Kirk and Spock swapping bodies due to an ill-fated experiment in sickbay. Roddenberry and Justman liked the idea, and encouraged the writer to try it again, this time in an outline form, however it was deemed a resemblance to another idea in development at the time, "Turnabout Intruder", and was eventually shut off. (These Are the Voyages: TOS Season Three, pp. 13-14)
"Tomorrow the Universe"
"Tomorrow the Universe" was written by Paul Schneider. The first draft was dated 1 March 1967 and was intended for TOS Season 2. The story dealt with a planet adopting Nazism – complete with swastikas and uniforms – after being culturally contaminated by a Federation visitor. Schneider's story bore a striking resemblance to John Meredyth Lucas' "Patterns of Force". Despite being submitted much later, Lucas' script was deemed to be much better and more developed, so Schneider's version was abandoned in favor of it. (These Are the Voyages: TOS Season Two) Schneider eventually filed a complaint to the Writers Guild of America. (These Are the Voyages: TOS Season Three, p. 512)
"Tomorrow Was Yesterday"
"Tomorrow Was Yesterday" was a sixty page outline written by David Gerrold in 1966, intended to be a two-part episode. Gerrold stated that he wrote the story as a two-parter for two reasons: a) "for more money" for him, and b) "it would have meant a greater spread of money in the budget for sets, costumes and actors."
According to Gene Coon, "Mr. Gerrold's outline was by no means inadequate. It is, as a matter of fact, very adequate." He further stated despite this, "to film the two-part story outlined here would probably cost $6-700,000" and that it was "too elaborate for television. What he has written is a good motion picture treatment for ideally a $2-3,000,000 picture."
Gerrold attempted to turn the outline in to a novel during the late 1960s, but he took the story into a different direction, retitling the manuscript as Yesterday's Children, which was later published by Dell Books in July 1972, and later renamed Starhunt. In 1980 he revisited his original story in the novel The Galactic Whirlpool. This story was completely unrelated to TOS: "Tomorrow is Yesterday".
The Enterprise comes upon a relic, a generation ship launched from Earth and long forgotten; the people on the ship have forgotten why they are aboard or that there is anything outside the ship's walls. There are two factions aboard fighting each other.
Story outlines by Philip José Farmer, dated 1 April 1966 and 5 April 1966. This was Farmer's third attempt to pitch a Star Trek story. The crew responds to a distress call from an uninhabited planet, finding a ragged old man with long beard living inside a jungle. They also find the ruins of an ancient city, complete with a statue of a god probably worshiped by a long-dead alien species. Returning to the Enterprise, the crew begins to experience memory lapses and behave strangely. Kirk and Spock finally develop "on-again-off-again" amnesia. It turns out that the Zaltons, the extinct alien race preserved their minds in the statue, and are now trying to take over the bodies of the Enterprise crew, who they lured to their planet. Finally Kirk and Spock (writing notes to each other whenever they get an idea, before they forget it) find a way to exorcise the aliens from the crew.
Both Gene Roddenberry and John D.F. Black deemed the outlines not interesting enough. (These Are the Voyages: TOS Season One, p. 362) The story is similar to TOS: "The Lights of Zetar", DS9: "Dramatis Personae", and VOY: "Memorial" in certain aspects.
Untitled Klingon two-parter
In a serialized essay across five volumes of 2006 trade paperback reprints of Alan Dean Foster's Star Trek Logs, adaptations of Star Trek: The Animated Series, the author explains that the original chapters he added to the adaptation of "The Counter-Clock Incident" (Star Trek Log 7), at the request of publisher Judy-Lynn del Rey, were first proposed as a two-part episode for the third live-action season, and held over for a potential fourth season. This tale features a Klingon commander named Kumara, whom Kirk first met during a Starfleet Academy exchange program. 
"Van Vogt's Robots"
"Van Vogt's Robots" was a story assigned by Gene Roddenberry to D.C. Fontana on 21 February 1968, based on A.E. van Vogt's two previously rejected story outlines, "The Machine That Went Too Far" and "Machines Are Better". However, it was never developed beyond the pitch, as Fontana left the series before she could work on this premise. (These Are the Voyages: TOS Season Three, p. 515)
The outline was based on a story idea featured in Roddenberry's original series proposal, entitled "Camelot Revisited", and dealt with an alien civilization (described as sort of a "modern-day Roman Empire"), based on chivalry and a strict honor code, against which the smallest breach results in serious consequences. Roddenberry thought this was an episode full of action-adventure, but it would be too expensive to produce, and assigned Kandel to develop another of his story ideas, "The Women", which ended up as "Mudd's Women". (These Are the Voyages: TOS Season One, pp. 69-70) A similar story concept ended up as TNG: "Code of Honor". A modern-day Roman Empire was featured in "Bread and Circuses".
"The Web of Death"
The Enterprise discovers its sister ship, the missing USS Momentous near planet Urus III, trapped in the cocoon of a giant insect. The creature also begins to cover the Enterprise in the same white substance, without much means of escape. Finally, Kirk and the crew manage to distract the creature into attacking the "dead" Momentous, and rescue its crew and themselves.
In a TV Guide article, Gene Roddenberry mentioned that Shatner delivered him a story outline written by him, and that he found it quite good, having a "good flow", despite his fears of it being terrible. The story was unproduced, though, probably because the series' budget couldn't allow the special effects it would have needed. 
"The Well of Death"
"The Well of Death" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28)
"What Tumult of the Mind"
The Enterprise encounters a primitive, telepathic society of sooth-sayers, frightened of outsiders, due to the dark images present in their mind. Kirk develops an interest for a young female seer, who claims that he is about to die soon. Kirk can't decide to dismiss this as simple superstition or take preventative measures against something he can't explain.
Story editor D.C. Fontana claimed that the story is a good one, and interesting science fiction, however it would need a complete revision to make it work as an hour-long television drama. Eventually, the script was rejected. (These Are the Voyages: TOS Season Three, p. 10)
Engelberg and Kahn's story is similar to another dismissed story idea, "The Foreseeable Future" by Jean Lisette Aroeste (see: above).