HBO’s documentary on the Church of Scientology, “Going Clear: Scientology and the Prison of Belief,” addresses rumors that have been swirling for years about the church. But the film's director, Alex Gibney, didn't tackle one of the biggest Scientology mysteries — the current location of the wife of Scientology leader, David Miscavige.

“At the end of the day, rather than doing stone skipping and covering as much as possible in a superficial way we chose to dig in on certain things,” Gibney told Business Insider on why he left the story out of the documentary.

Scientology leader David Miscavige.

Gibney also told BI that though there was a longer version of the film that included more details about Scientology, the story of Miscavige’s allegedly missing wife, Shelley, was never investigated and they never filmed anything about it.

Shelley has allegedly been missing since 2006, reportedly following an incident where she filled several job vacancies without her husband’s permission, as initially reported by The New Yorker’s Lawrence Wright (who would go on to write “Going Clear: Scientology, Hollywood & The Prison of Belief,” the book that inspired Gibney’s film).

To be clear, a spokesperson for the Church of Scientology has denied to Business Insider that Shelley is missing. That spokesperson called the HBO documentary a "propaganda film." (See the full statement at the end of this article.)

Church spokespeople have repeatedly denied through the years that Shelley is missing, Vanity Fair reported last year, but the rumors of her absence persist.

In 2012, Steve Hall, a former Scientologist, told BI that he believes she’s staying at the little-known “Church of Spiritual Technology,” a remote forest compound in Twin Peaks, California, near San Bernadino.

One of the buildings at Scientology's Twin Peaks compound. Angry Gay Pope After actress Leah Remini, a 30-year vet of the church, left Scientology in 2013, she reportedly filed a missing persons report for Shelly with the Los Angeles Police Department. Her suspicion reportedly began years ago after noticing Shelly wasn’t with her husband at the 2006 wedding of Tom Cruise and Katie Holmes, in which David was Cruise’s best man.

Around the time of Remini notifying the police, the journalist Tony Ortega, a longtime critic of the church with his blog "The Underground Bunker" (who is also featured in "Going Clear"), reported that Shelly is at the church’s secret compound in the mountains of Los Angeles.

Here's why Shelly is allegedly banished, according to Ortega:

“Early in 2004, at Scientology’s International Base — a secretive, 500-acre compound about 90 miles east of Los Angeles, near the town of Hemet — Miscavige took his ideas about discipline to strange new lengths. A few dozen executives he wanted to punish were locked into a set of rooms that had been an office, and “The Hole” was born. Over the next several years, even more executives who had fallen from his favor were added to the bizarre and harsh office-prison, reaching about 100 total prisoners. Around that time, Miscavige also became obsessed with the base’s “Org Board.” It was a roster of jobs that Miscavige wanted filled, but for some reason his underlings could never fill out the empty slots in the roster to his satisfaction. People who worked there at the time tell us that Miscavige’s tirades about the org board were maddening and relentless. Then in 2005, Miscavige did something surprising — he traveled to nearby Los Angeles to work on a publishing project, and Shelly stayed behind at the base. People who worked at the base tell us it was the first time they remembered seeing the couple apart. Shelly took advantage of her husband’s absence to fill in the org board that had proved such a headache. She also made progress on another project Miscavige had been promising to start by moving his belongings out of a set of buildings called the ‘Villas.’ She moved his things into another set of rooms called ‘the G’s,’ so the Villas could be renovated… When Miscavige returned from Los Angeles and found the org board filled and his belongings moved, he erupted. A week later — which was sometime late in 2005 or early in 2006, our sources tell us, Shelly vanished.”

Business Insider reached out to Scientology to comment on Shelly's alleged disappearance:

"The false allegation about Mrs. Miscavige was debunked by the Los Angeles Police Department in a statement two years ago," a spokesperson for the church told BI in a written statement. "The police declared the rumor 'unfounded' and she continues in the Church as she always has. The notion that Mrs. Miscavige is missing is a conspiracy theory among Alex Gibney and Lawrence Wright's unsavory sources. The rumor has resulted in the disgraceful harassment of Mr. and Mrs. Miscavige. It is disgusting. The Church has made information available about Mr. Gibney’s film at www.freedommag.org/hbo."

The Church of Scientology also disputed the existence of a place called "The Hole" to BI:

"This is another tired, false and offensive allegation. The only 'hole' at the Church property being referred to is on the golf course. This again sources to the same small group of liars. This false propaganda was exposed as a lie in our video at freedommag.org/hbo/videos/exterminating-gibneys-propaganda.html."

But the so-called "hole" is featured in one of the most chilling scenes in “Going Clear.”

Former Scientology executives who claim to have been in the hole said Miscavige gathered the group in a room, put empty chairs in the middle of it, and told them to play musical chairs. He allegedly told them when one chair remained that person was allowed to stay in their position, and everyone else would be sent off to remote locations.

According to the film, Miscavige started playing the music, Queen’s “Bohemian Rhapsody,” and the staff began circling the chairs. When the music stopped the staff battled for seats. The fewer chairs that remained throughout the game, the more aggressive people were to get a chair, allegedly leading to punching and shoving. After one person finally remained, Miscavige told everyone in the room that he changed his mind and everyone was allowed to stay.

The group stayed in the hole and continued work on the org board, according to the film.

Mike Rinder in "Going Clear." HBO

“This just is David Miscavige,” Mike Rinder, a former executive of Scientology who is featured in “Going Clear” and was involved in the alleged musical chairs incident, told reporters at HBO’s offices last week. “His personality type is sociopath. He takes a lot of things that in the hands of someone else would be innocuous and uses those as tools of weapons to abuse people.”

Scientology also disputed Rinder's comments. Rinder has since responded to BI to address the below comments from Scientology:

Scientology: "The source for these allegations, and Gibney’s primary subject, Mike Rinder, is talking about himself. Mr. Gibney and now yourself, due to prejudice and bias, have obliged in revising history for self-admitted suborners of perjury, perjurers and obstructers of justice."

Rinder: "I am no 'self-admitted suborner of perjury, perjuries and obstructer of justice' and I challenge them to produce whatever documents they say they have. This is a typical scientology sleaze. They claim [fellow former Scientology executive] Marty Rathbun admitted to doing this WHILE HE WAS EMPLOYED BY THE CHURCH and then ascribe it to me."

Scientology: "Mike Rinder admitted in a January deposition to the exact opposite of what he says to Mr. Gibney in the film and now to you."

Rinder: "No idea what they are referring to. And they don't cite the deposition or any specific statements that are 'the exact opposite.' Why not? They published portions of the deposition on their Freedom website? The entire transcript is available on Tony Ortega's site."

Scientology: "He’s also a tainted source because he’s admitted to being paid by law firms seeking to score a payday suing the Church. You should know that just today the Church won a decisive victory in the case Rinder and his attorney clients had been hoping to hit the jackpot on."

Rinder: "Yes, I was hired as a consultant by several lawfirms. I testified in this deposition they refer to that it composed 10% of my income last year."

Scientology: "Rinder’s domestic abuse is documented by his ex-wife, brother, daughter and his ex-wife’s surgeon, and all of this would have been relevant to the film since Gibney shamelessly has Rinder lie about his ex-wife yet he didn’t ask her for comment or to sit for an interview, even when she was in New York to see him."

Rinder: "The alleged abuse is also documented by the Pinellas County Sheriff's Office and on BBC TV. It's covered in my blog. I didn't lie about my ex-wife. I didn't even MENTION that she came to Florida with 6 other people, followed me and assaulted me in the parking lot of a doctor's office. And the Sheriff's Office did NOT find any 'domestic abuse.'"

Scientology: "Alex Gibney and HBO cynically repackaged Mike Rinder into the poster boy for their new propaganda film. They flew Rinder around the country in five-star luxury to shill for their religious hatred, never mentioning that Rinder was expelled from his former religion for gross malfeasance. They hid that Mike Rinder can’t hold a job and his only source of income is payment for attacking Scientology. Gibney knew all this but relevant facts would have popped the phony bubble of legitimacy Gibney created around his 'star.'"

Rinder: "Funny, the same deposition they refer to, I told them EXACTYLY what I did for a living. And that only 10% of my income came from consulting law firms on scientology cases. Somehow that becomes 'can't hold a job' and 'my only source of income is payment for attacking scientology.' These people lie even when they don't need to. This isn't even relevant to any specific claim in the film, but they just have to go out of their way to somehow proclaim me as being 'unable to hold a job'? My current activities in life have no bearing on what I have to say about my experiences inside scientology."

Scientology: "And, at a time when religious hatred is spreading through the world and inciting violence, it is also irresponsible to release any film about religion with someone so obsessed with inciting hatred as Mike Rinder, an admitted liar and suborner of perjury, a paid anti-religionist and a domestic abuser. http://www.freedommag.org/hbo/videos/mike-rinder.html"

Rinder: "Finally, why don't they address ANY of the statements I make in the film? Not one of them. Instead, they respond with ad hominem attacks. I will tell you why that is -- they CANNOT refute the truth. And they are bound by their own policy to 'always attack, never defend.'"

Scientology: "Mr. Miscavige has been successfully leading the Scientology religion for more than a quarter of a century during which the Scientology religion has expanded faster in the last 10 years than in its previous 50 years combined. Scientology parishioners worldwide hold him in the highest esteem for what he is doing for the religion."

Rinder has also included a post on his blog addressing the allegations Scientology has made against he and "Going Clear."

This is not Gibney’s first time examining the alleged abuse of power. He was nominated for an Oscar exposing the corrupt acts by the heads of Enron (“Enron: The Smartest Guys in the Room”), won one looking at US torture tactics ("Taxi to the Dark Side"), and has done films on the illegal methods done by “Casino Jack” Abramoff (“Casino Jack and the United States of Money”), the untruthful statements made by Lance Armstrong (“The Armstrong Lie”) and the questionable motives of Julian Assange (“We Steal Secrets: The Story of WikiLeaks”), not to mention the illegal sexual conduct by the Catholic Church (“Mea Maxima Culpa: Silence in the House of God”).

With his history of examining infamous characters, how does Gibney see Miscavige?

“He’s a true believer who is doing everything he can to protect his religion,” Gibney told BI. “And in that way it may be even more terrifying because at some point you can sit someone down who is not a true believer and say ‘let’s do a risk/reward analysis.’ That’s not something he’d be willing to engage in.”

"Going Clear" opens theatrically in limited release today and airs on HBO March 29.

