In late 1969, three story outlines were suggested by Don Christensen, while the series was imagined as involving some specifically educational material in each episode and being set aboard the training ship Excalibur, where each of the main characters would have a similar-looking child counterpart. An analysis of the outlines was included in a three-page memo that, on 15 October 1969, was sent from Philip Mayer (director of special programming for Paramount) to Filmation co-founder Lou Scheimer. One of Mayer's comments was: "I think as long as we're only doing three outlines, each one of them should be special." (Star Trek Magazine Souvenir Special, pp. 55 & 56)
"The Space Cocoon"
This was the first of the story outlines that Philip Mayer critiqued in his memo to Lou Scheimer. Mayer stated, "Generally I think the outline is ok. Christensen's concern for the small size of the children doesn't bother me at all. I'd be apt, in this story and any other outlines at all, to call the training ship by its name. As we discussed, the whole crab/spider business won't be acceptable, so should be changed before submission. I had no sense of real interrelationship what-so-ever between the old and young characters in this episode. The Spock/Steve relationship really didn't work at all. Spock gets knocked out and Steve goes off. To heighten the relationship, probably Steve should have stayed with Spock and been instrumental in his recovery. There was [also] no indication at all of the educational stuff." (Star Trek Magazine Souvenir Special, p. 56)
"The Impossible Rainbow"
Philip Mayer found this plot outline more likable than that of "The Space Cocoon", commenting, "It seems to be more relevant as a children's show. There's a better cross between fantasy and reality with the rainbow and the 'quiet boy' character. There is some educational material in this show, but it's a bit hidden. All that has to be done is to relate it to [Dr. McCoy's] counterpart Bob. I like the trogs." (Star Trek Magazine Souvenir Special, p. 55)
Philip Mayer thought this story outline was "ok," essentially. "As in the other two outlines, the educational material has to be punched out and interrelationships between the characters has to be handled better," he remarked. "Somehow, the whole thing seems ordinary. There's no real point of view to this story, or maybe it's not really very special." Mayer concluded his notes on this Klingon-related outline by stating that he was "sure something is" missing. (Star Trek Magazine Souvenir Special, p. 55)
Quantum black holes
After Dorothy "D.C." Fontana – story editor and associate producer for the animated Star Trek series – invited science fiction author Larry Niven to write for the series, he made his first attempt at concocting a story treatment, which involved quantum black holes and a group of highly sophisticated aliens. Niven later recollected, "I feared (groundlessly) that nobody at Filmation would see their chance to use real aliens rather than actors in rubber suits. So I wrote a story treatment using Outsiders (built like a black cat-o'-nine-tails, using photoelectric metabolism at near absolute zero) and quantum black holes. For Saturday morning TV!" Fontana advised him that the story treatment wouldn't work. He later admitted, "Dorothy Fontana was right: I was aiming over the audience's heads." (Playgrounds of the Mind) This initial plot concept, however, became the basis for Niven's story "The Borderland of Sol", which was first printed in the January 1975 issue of Analog magazine and won the 1976 Hugo award for best novelette. 
Larry Niven second attempt
The second story that Larry Niven proposed for the animated Star Trek series was considered to be "too bloody." He thereafter went on to successfully adapt a short story he himself had written (entitled "The Soft Weapon") into the episode "The Slaver Weapon". (Playgrounds of the Mind)
"The Patient Parasites"
Temporarily considered for the animated series' first season, "The Patient Parasites" entered development after D.C. Fontana contacted Russell Bates, in 1973, with news that the series was in the works. (The New Voyages 2; ) Fontana made it clear to Bates, a Kiowa Native American, that she wanted him to write a script for the forthcoming animated production. Having submitted an ultimately undeveloped episode for the original series, Bates was eager to accept her invite. (The New Voyages 2) He recalled Fontana's expectations for the animated episode; "She had always wanted to see an Indian Star Trek crewman and a story about 'the little men from the stars' that Native Americans note in their legends."  Bates worked hard on the script, over a period of two weeks, before sending it to Fontana. (The New Voyages 2)
The proposed script concerned a volatile machine known as Finder, which had been dispatched with instructions to acquire "knowledge, and the wisdom to use it" for notoriously patient masters that, according to extreme probability, were now extinct. Finder imprisoned several members of a landing party from the Enterprise on a planet where the machine was, but when Captain Kirk taught Finder that the selfishness of its masters had led them to ruin, the machine self-destructed while the captives were rescued. The Enterprise then safely departed the planet. The script included the character of Native American officer Dawson Walking Bear and the story's title was an allusion to Finder's masters, which were considered figuratively parasitic, such as Dr. McCoy exclaiming to Kirk, "Jim, they're parasites! They steal technology and never have to develop it for themselves." (The New Voyages 2)
The script was returned to Russell Bates, D.C. Fontana being critical of the teleplay. (The New Voyages 2) The story was found to be lacking in two key areas. Firstly, Bates had not done his job by delivering the kind of story that Fontana had requested, since it was merely a generic Star Trek plot he had written rather than an Indian story. (Starlog Issue #159, p. 27; ) Secondly, the narrative did not take advantage of the extreme possibilities inherent in the animated format, regarding such concerns as actors, costuming, sets and locations. (Starlog Issue #159, p. 27) Bates remembered of the script, "It was too close to live film, lacking the scope that animation can bring." Fontana told him that, if given greater length, the story very easily could have been done for the original series, a comment that Bates later admitted to having "cherished." (The New Voyages 2)
Upon Russell Bates meeting David Wise at the Clarion Science Fiction Writers' Workshop in 1973, they realized that Wise, having been an animator in his pre-teen years, could help Bates by adding a useful perspective to his pitches to D.C. Fontana. "I think, during the course of the Clarion Workshop that summer," said Wise, "he was pitching ideas to her long-distance, and getting turned down [....] And I saw that he was pitching stories to her that were basic Star Trek stories about mind parasites and things like that." ("How Sharper Than a Serpent's Tooth" audio commentary) When they later co-wrote the episode "How Sharper Than a Serpent's Tooth" for the second season of the animated series, Bates reused Dawson Walking Bear as a prominent character of that installment. "But 'The Patient Parasites' preceded it as the first attempt to do several things," noted Bates. "1, write ST in half-hour form and still be faithful to the show's original quality; 2, introduce an Amerindian character aboard the Enterprise [...] and, 3, finally write for ST as I set out to do back in the sixties." Bates considered "The Patient Parasites" to be "a story without a home," until he saw the book The New Voyages; he included a modified version of the script in the second volume, The New Voyages 2, for which he substituted Sulu for Dawson Walking Bear. (The New Voyages 2)
In 2005, Russell Bates gave permission to startrekanimated.com's Kail Tescar to adapt his original script into comic book form. Following the script, Ensign Walking Bear was written back into the story, and a newly-promoted Lieutenant Chekov was written in as the Enterprise's new security chief.
In 1973, NBC publicist Fred Bronson submitted a story which dealt with World War II and was called "War Game", which was his first attempt at submitting a Star Trek script. His concept for an installment of the animated series had to be written under a pseudonym, because his contract with NBC did not actually permit him to write for the series. Bronson stated, "The childrens' programming department at NBC thought that World War II wasn't a fitting subject for children, so it was turned down." He was concerned people might have discovered that the pen name under which he wrote this story was an alias for him, so Bronson used a different assumed name when submitting "The Counter-Clock Incident", the second story he proposed for the animated Star Trek series, which was produced as its series finale. (Starburst Special #29, p. 55)