South Park had previously parodied Scientology in a spoof at the 2000 MTV Movie Awards. The MTV short was titled "The Gauntlet" and included "John Travolta and the Church of Scientology" arriving in a spaceship to defeat Russell Crowe (as a gladiator) and attempt to recruit the boys into Scientology. Travolta, along with his fellow Scientologists, was depicted as a Psychlo, as he appeared in the film Battlefield Earth. They had also made fun of Scientology in an earlier episode, titled "Super Best Friends", in which David Blaine formed his own cult, called "Blaintology". Parker and Stone have acknowledged that this is meant to be a reference to Scientology.  Parker stated that Isaac Hayes' membership had previously kept the show's creators from writing a full episode which parodies Scientology. However, the decision to ultimately produce a South Park episode satirizing Scientology was partially inspired by the friendship the show's creators have with Penn Jillette. Jillette was originally planning to do an episode of Bullshit! based on Scientology, but Showtime prohibited him from doing so to avoid the possibility of legal action from the Church of Scientology. Parker commented, "We're going, That's fucked up. And hearing other people say, 'You can't do that' - you can only say 'You can't do that' so many times to Matt and me before we're gonna do it. Finally, we just had to tell Isaac, 'Dude, we totally love working with you, and this is nothing personal, it's just we're South Park, and if we don't do this, we're belittling everything else we've ripped on.'"  Although some questions were raised prior to the episode's screening about whether it was wise to take swipes at Cruise and Scientology, Comedy Central declared that it supported Stone and Parker. A Comedy Central spokesman told Radar magazine in November 2005 that "they are free, and have been, to satirize anybody and anything they want to. They've made fun of MTV, they've made fun of Viacom, they've made fun of Comedy Central, and we've never interfered with them."  During production on the episode, investigative journalist Mark Ebner served as a consultant to Matt Stone and Trey Parker. Ebner had previously authored The New York Times best seller Hollywood, Interrupted, which includes an analysis of the Church of Scientology and its effects on the culture in Hollywood, and has a chapter on Tom Cruise and John Travolta's relationship to Scientology. On the official Comedy Central website for the South Park episode, it is asserted that the section of "Trapped in the Closet" that explains Scientology's portrayal and beliefs was not exaggerated: "Nothing about what you see here is exaggerated in the slightest. Seriously." The title is a reference to the R. Kelly song of the same name, and a depiction of R. Kelly appears in the episode to sing a parody of it.

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