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Gay Star Trek storylines have been written—such as the Star Trek: The Next Generation episode, “Blood and Fire” by David Gerrold—but it was never put before cameras. In this episode, written back in 1987, the crew of the U.S.S. Enterprise encounter a derelict spaceship infected with a dangerous pathogen, known as Regulan Bloodworms, capable of killing the infected within hours. This episode was to be a 24th century allegory to the HIV/AIDS scare of the 1980s. One of the main reasons, however, this episode was never put into production was because two of the episode's characters, Freeman and Eakins, were intended to be a gay couple.

The official explanation for the episode's cancellation was because of studio concerns. Gerrold stated in an interview with Mark Altman for Cinefantastique that he believes the episode dealt with homosexuality in a “blatant” manner. He says the feedback from the staff was either encouraging or concerned. “There was a paper trail a yard wide and a mile long on everything and the memo on this was half that. People complained the script had blatant homosexual characters. Rick Berman said we can't do this in an afternoon market in some places. We'll have parents writing letters.

The other half of the memos were, from people like Dorothy Fontana and Herb Wright and Bob Lewin, who said this is a very strong script. I'm not making Rick Berman a villain because he also acknowledged the technical aspects of the script were right on the nose for what the show needed to be. But Rick Berman was the studio guy. He was watching out for the studio's interests.”

Three episodes, in particular, are labeled Star Trek's “gay” episodes. The first is a Star Trek: The Next Generation episode called “The Outcast” which dealt with an androgynous species (cast entirely of female actors) known as the J'naii who do not have typical gender roles of male and female. Those that do identify as either/or are seen as abnormal and sent to rehabilitation centers. Riker falls in love with Soren (Melinda Culea), a young J'naii who identifies with the female gender. When he attempts to rescue her, she eventually decides to stay. Gay viewers felt the episode cheated given all the actors playing the J'naii were obviously women.

“The Host” also dealt with homophobia presented as subtext. In the episode, Dr. Beverly Crusher falls in love with a Trill ambassador, Odan, who later dies. His new host turns out to be a woman (played by Nicole Orth-Pallavacini), prompting Dr. Crusher to end the relationship. It is said that Gates McFadden, who played Dr. Crusher, attempted to change the ending of this episode, but was overturned by studio execs.

McFadden isn't the only actor who objected to an episode's homophobic overtones. A Salon article from 2001 reports that in the Star Trek:The Next Generation episode “The Offspring” actor Whoopi Goldberg (Guinan) refused to say the line “When a man and woman are in love...”. She opted instead to say “When two people are in love.” Said Goldberg, “This show is beyond that. It should be." It was also decided on set that the background of the scence show a same-sex couple holding hands, but one of the show's producers made sure that didn't happen.

The final gay Trek episode was Star Trek: Enterprise's episode, “Stigma”, in which T'Pol (Jolene Blalock) contracts a rare mental disorder, Pa'nar Syndrome that is portrayed as a version of the HIV/AIDS (of which she is eventually cured).

Berman told TrekWeb in April of 2003 that “Stigma” was, “supposed to be our gay episode, but we sort of copped out.” Some critics of the episode also felt synonymously linking the HIV/AIDS virus specifically with the GLBT community to be questionable at the very least.

There have been other Star Trek episodes perceived as having gay-ish themes. One that misfired was 1998's “Profit and Lace”—written by Ira Steven Behr & Hans Beimler. Here the context of male homosexuality and transgenderism are set up as comedic and insulting instruments. Producers, fans, and even the story's main actor, Armin Shimmerman consider this Deep Space Nine episode to be one of its worst.

In its defense, Deep Space Nine has also portrayed homosexuality in a (somewhat) positive light. In the episode, “Rejoined” written by Battlestar Galactica producer, Ronald D. Moore, Trill Lt. Jadzia Dax (Terry Farrell) is reunited with Lenara Kahn (Susanna Thompson), a lover from a previous life (Trills being a symbiotic species who live many lifetimes from host to host). Rekindling a romance with previous hosts is taboo and punishable by exile. In what is undoubtedly a metaphor for modern-day homophobia, Jadzia defies the law, and engages in the first ever same-sex kiss in Star Trek's history. But, in the end, Len ara Kahn leaves and Jadzia Dax “comes to her senses”.

This episode is both praised and criticized by fans. Gay followers of the show feel the romance wasn't homosexual in nature as Dax's previous host was male, while Kahn's was female.

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