It was billed as a cast recording for a proposed musical of the same name, which was ultimately not produced by Zappa, but later performed partially in 2003, ten years after his death.

The album's storyline is inspired by Broadway theatre, AIDS, eugenics, conspiracy theories, feminism, homosexuality and African American culture.

The story within a story is a satire of a White Anglo-Saxon Protestant couple, Harry and Rhonda (actually played by Italian-Americans), who attend a play performed by the "Mammy Nuns", and find themselves confronted with their pasts: Harry presented as a homosexual boy, Rhonda presented as a sex doll brought to life.

[2] Thing-Fish also drew conceptual themes from AIDS, feminism, gay chic, conspiracy theories and issues of class, greed and race.

[4] As the recording process continued, Zappa brought in revised scripts and improved the work by editing or changing aspects with which he was dissatisfied.

[1] Subsequently, Thing-Fish dialogue appeared on the album Frank Zappa Meets the Mothers of Prevention, during the piece "Porn Wars".

So we take it one step further and they're concocting the special disease which is genetically specific to get rid of 'all highly rhythmic individuals and sissy boys.'

[...] I asked Frank if he had ever heard of this guy, and he said, 'No,' so I started giving him examples of Dunbar's work, and eventually, that ended up being a big influence on the Thing-Fish dialect.

[2] It is revealed that Harry had become a homosexual as a result of the women's liberation movement, which caused him to lose all sexual desire for women; the younger versions of the characters are portrayed in the characters "Harry-As-A-Boy" and "Artificial Rhonda", with the young Rhonda being portrayed as a rubber sex doll, while her older counterpart becomes increasingly fascistic and feminist towards the end of the story.

[11] As Harry and Rhonda express admiration for the "performance" of the Evil Prince, an early version of Zappa's Synclavier composition "Amnerika" is heard.

[18] The Evil Prince, defeated at his own hands, delivers a soliloquy in the form of a Broadway piano ballad, "Wistful Wit a Fist-Full".

[1][20] MCA produced a test pressing of the triple LP set, but withdrew their distribution after a woman in their quality control department became offended and upset by the album's content.

[1][20] Zappa wrote a "warning" which appeared on the inner sleeves of these albums, as well as Frank Zappa Meets the Mothers of Prevention, which stated that the albums contained content "which a truly free society would neither fear nor suppress", and a "guarantee" which stated that the lyrics would not "cause eternal torment in the place where the guy with the horns and pointed stick conducts his business.

All other CD releases contain modifications, edits, re-equalization, and some minor remixing (the most significant difference—Johnny "Guitar" Watson's commentary during "He's So Gay"—was not implemented immediately).