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This Is One Of The Most Shocking Scientology Stories Not In 'Going Clear'

There is lot of unsettling information when it comes to the Church of Scientology, all of which is explored in Alex Gibney’s latest documentary, “Going Clear: Scientology and the Prison of Belief.” But there’s one story that was left out of Gibney’s film, which premiered this past Sunday on HBO: Where is Michele “Shelly” Miscavige?

Miscavige is the wife of the Church’s current leader, David Miscavige, and member of the Church’s Sea Organization (Sea Org). According to Lawrence Wright’s book on which Gibney’s film is based, she disappeared in June 2006 and has not been seen publicly seen August 2007. Her official whereabouts are still unknown.

According to investigations by Wright and journalist and Scientology critic Tony Ortega, while David Miscavige was away in 2006, Shelly Miscavige appointed positions in the Chuch’s Org Board. It was a task her husband had been struggling with and had reportedly threw “maddening and relentless” tirades over. In Going Clear, Wright reveals that when David Miscavige returned home, Shelly’s mood had noticeably changed, according to her brother-in-law, John Brousseau. Soon after she disappeared.

Actress and former Scientologist Leah Remini drew the most public attention to Shelly Miscavige’s vanishing when she took action and questioned the Church. According to former Sea Org member Mike Rinder, Remini asked about Shelly Miscavige’s whereabouts at Tom Cruise and Katie Holmes’ 2006 wedding. Remini was reportedly scolded for asking about it and later “was put through interrogations and blacklisted within the church,” according to the New York Post.

After defecting from the Church in June of 2013, Remini filed a missing person report on the leader’s wife. Hours after filing the report, the Los Angeles Police Department ruled it “unfounded.” The LAPD also did not comment to Wright about Shelly Miscavige’s whereabouts.

While Wright reported on Shelly Miscavige’s disappearance in his book, it is not mentioned in Gibney’s documentary. At a press screening of the film last week, the director addressed the omission saying, “The Shelly Miscavige story, had we profiled different kinds of people, might have made it into the final film.” Although Gibney had hours of extra footage that he ended up cutting — which he said he would ideally like to release with HBO in the future — the director told Business Insider that none of the filmed material involved the Church leader’s missing wife.

Ortega echoed this to The Huffington Post over email on Monday, writing that he believes Shelly Miscavige was left out of the film so viewers could walk away with two important questions: “Why does Scientology still have tax exempt status, and how can Tom Cruise remain silent?”

The journalist, whose reporting has broken news and revealed details about Miscavige’s possible whereabouts, added that even if she were found, he doesn’t believe she’d willingly leave the Church. “Her story would take a considerable amount of time to tell, and ultimately, does she really want to be rescued? I’m doubtful about that.”

While the Church hasn’t commented on Shelly Miscavige’s whereabouts, Brousseau told Ortega that she’s been at the secretive Church of Spiritual Technology headquarters in Hemet, California. Sources have told Ortega that she is working there, archiving Hubbard’s printed words on steel plates.

But Shelly Miscavige is just one of the many shocking Scientology stories left out of “Going Clear.”

“Ultimately we were focusing on our characters,” Gibney said at the screening, “and rather to do a bit of stone-skipping and trying to cover everything, we tried to focus.”

The Church has publicly spoken out against the film. Reps for Remini said the actress was not available to comment.

“Going Clear: Scientology and the Prison on Belief is now playing in select theaters and on HBO.