In Madrid in 1980, Enrique Goded, a young film director, is looking for his next project when he receives the unexpected visit of an actor looking for work. The actor claims to be Enrique's boarding school friend and first love, Ignacio Rodriguez. Ignacio, who is using now the name Ángel Andrade, has brought with him a short story titled "The Visit" hoping that Enrique would be interested in making a film out of it giving him the starring role. Enrique is intrigued since "The Visit" described their time together at the Catholic school and it also includes a fictionalized account of their reunion many years later as adults.
One week before her vaginoplasty, Sabrina 'Bree' Osbourne (Felicity Huffman) receives a phone call from Toby Wilkins (Kevin Zegers), a 17-year-old jailed in New York City. He asks for Stanley Schupak (Bree's birth name), claiming to be her son.
Teenager Mary Cummings (Jena Malone), who has "been born again her whole life," is about to enter her senior year at American Eagle Christian High School near Baltimore. She and her two best friends, Hilary Faye (Mandy Moore) and Veronica (Elizabeth Thai), have formed a girl group called the Christian Jewels. Mary’s "perfect Christian boyfriend" Dean Withers (Chad Faust) tells her, as they’re swimming underwater, that he thinks he's gay. In her shock, Mary hits her head in the pool and has a vision in which Jesus tells her that she must do everything she can to help Dean. Hoping for a sign, Mary goes to a shooting range with Hilary Faye, who has a "spiritual solution for everything" and tells Mary (not knowing about the situation with Dean) that if all else fails, Jesus could still restore their "spiritual and emotional virginity." Believing that Jesus will restore her purity, Mary sacrifices her virginity to have sex with Dean in an attempt to restore his heterosexuality.
1971: Arnold (Harvey Fierstein), a New York City female impersonator, meets Ed (Brian Kerwin), a bisexual schoolteacher, and they fall in love. Ed, however, is uncomfortable with his sexuality and he leaves Arnold for a girlfriend, Laurel.
Father Greg Pilkington, newly assigned to St. Mary's parish in inner-city Liverpool, is startled to discover Father Matthew Thomas is engaged in a sexual relationship with rectory housekeeper Maria Kerrigan. Moreover, Father Thomas is a left-wing radical and an outspoken proponent of Liberation Theology, leading him to constant clashes and bickering with the Bishop—who nevertheless appreciates his abilities.
Noam, a young Israeli reservist working at a checkpoint while on reserve duty, is crushed when he witnesses a Palestinian woman giving birth to a dead baby; he also locks eyes with a young Palestinian man there, Ashraf. He then gets back to Tel Aviv as he has finished his military service. There he shares a flat with another gay man, Yali, and a woman, Lulu, who works in a soap shop. The three roommates live a generally bohemian life.
Elder Aaron Davis, a young Mormon from Pocatello, Idaho, is sent to Los Angeles with three other missionaries to spread the Mormon faith. They move into an apartment next to openly gay party boy Christian Markelli and his roommate Julie, an aspiring singer. Christian and Julie work as waiters at Lila's, a trendy restaurant owned by retired actress Lila Montagne.
Trembling Before G-d interviews and follows several gay and lesbian Orthodox Jews, many only seen in silhouette, and also interviews several rabbis and psychologists regarding their views on homosexuality in Orthodox Judaism. The film repeatedly returns to several characters:
Lilies is set in a Quebec prison in 1952. Jean Bilodeau (Marcel Sabourin), the local bishop, is brought to the prison to hear the confession of Simon Doucet (Aubert Pallascio), a dying inmate. But Doucet in fact has a very different revelation for Bilodeau: he has enlisted his fellow inmates to stage a play set in 1912, when Bilodeau and Doucet were childhood friends.
Yossi (Ohad Knoller) commands a company of soldiers in the snow-covered mountains near Lebanon. In secrecy, he leads a passionate romantic relationship with his second-in-command officer, Lior (Yehuda Levi), who is called Jagger by everyone for his rock star-like handsomeness and his lip-syncing Mick Jagger.
Yossi, a 34 years old closeted gay man, works as a cardiologist in a hospital in Tel Aviv. He has never completely recovered from the death of the love of his life, ten years before. Unhappy in his personal life, Yossi has thrown himself into his work. When not on call, the physician finds comfort in greasy take-out noodles and soft core gay porn.
Director Reed Cowan, who is a former Mormon missionary, "planned on making a film about gay teen homelessness and suicide in Utah, but switched his focus to Mormon ideology because of how it contributes to the homophobia that causes these problems". The film focuses on the wealth and power of the The Church of Jesus Christ of Latter-day Saints, and how the Church uses the National Organization for Marriage to advocate for denial of rights to lesbian, gay, bisexual, and transgender (LGBT) Americans. It states that LDS Church leader Thomas S. Monson asked to ensure the passage of the controversial California Proposition 8. It also states that many homeless people in Utah are LGBT teens who were abandoned by their Mormon parents.