Star Trek is..., the very first series outline, listed a number of short ideas for episodes, some of which were later worked out. 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 his book The Trouble with Tribbles.
Gerrold adapted his story for the third volume of Star Trek: The Manga.
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.
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 obliged, giving 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
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. Entitled "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) 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)
For They Shall Inherit
Undated story outline by Jerome Bixby.
Undated story outline by science fiction writer Hank Stine.
Undated story outline by Charles Parker.
The Forseeable Future
From the First Day To The Last
Shelved envelope for "The Menagerie" by John D.F. Black, delivered 8/12/1966
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 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 re-wrote the episode to become a comedy. The re-written 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 shit". He told Roddenberry to "read it and weep". Roddenberry agreed, and the episode was never produced. (Star Trek Monthly issue 26, p. 24)  
Image Of The Beast
Story outline by science fiction writer Philip José Farmer dated 27 March 1966. Though he may or may not have reworked the Star Trek proposal for this, Farmer would subsequently publish the dark erotic science fiction/horror novel also entitled Image of the Beast.
"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
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.
The Land of Counter-Pain
"The Land of Counter-Pain" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28)
The Lost Star
Machines Are Better
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. vanVogt and Jack Williamson was delivered on 4/5/1966, and a revised version was delivered by the same writers on 4/20/1966. Story cut-off was exercised on 4/27/1966.
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, 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").
"Miss Gulliver" 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)
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. The year was 1968 and David Gerrold, the writer of both tribble-related outings, was twenty-four years old. (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
The Orchard People
The Pastel Terror
Perchance To Dream
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 colours out of synchronization.
Return To Eden
Rites Of Fertility
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. 
The Search For Eternity
The Shadow of Space
"The Shadow of Space" was written by Philip José Farmer in 1966.  The story involved the Enterprise traveling outside the universe. Farmer published a prose adaptation of the idea, under the same title, but with names changed from the Star Trek version for copyright reasons. The story first appeared in the science fiction magazine Worlds of If and subsequently in single author collection of Farmer's short fiction.
Shore Leave II
Sister In Space
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 another proposal, "The Shadow of Space", Farmer later used the idea as the basis of a published short story, 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. 
Undated outline by Robert Bloch.
Space Moby Dick
"Space Moby Dick" would have involved the crew hunting a space-borne deadly monster through the galaxy. (Star Trek Monthly issue 26, p. 28) Obviously, the episode's name was most likely a working title, owing to its use of the name Moby Dick.
The Stars of Sargasso
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)
Tomorrow the Universe
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.
The World of Star Trek revealed a story premise that DeForest Kelley had always wanted to see, 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."
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 added a footnote to DeForest Kelley's premise, stating, "As a matter of fact, the idea was one that very definitely had been considered. A script version had even been written. And rewritten. And rewritten. The story involved a planet where blacks were the masters and whites were the slaves, 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."
The basis of this episode was probably a story premise in Roddenberry's 1964 proposal Star Trek is..., entitled Kongo, about a planet with the "Ole Plantation days" with reversed roles of blacks and whites.
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)
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. 
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 manages 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 through, probably because the series' budget couldn't allow the special effects it would've needed. 
The Well of Death
"The Well of Death" was an abandoned Star Trek episode. (Star Trek Monthly issue 26, p. 28)