OF all the controversies surrounding the Church of Scientology there are two mysteries which continue to disturb and fascinate.

One is the whereabouts of former Scientology first lady Michele “Shelly” Miscavige — wife of supreme leader David Miscavige — who vanished in bizarre circumstances 11 years ago. The other is the untimely death of longtime member Lisa McPherson in 1995.

The cases are the subject of a new documentary called “Scientology’s Vanished Queen”, based on a 2014 expose by Vanity Fair, which premiered in the US on Monday.

According to the documentary, the tragic fate of both women was sealed when they began experiencing symptoms of mental illness, sending the notoriously anti-psychiatry hierarchy into damage control.

Lisa, who joined the church in her late teens, was just 35 when she suffered a fatal pulmonary embolism after undergoing a gruelling 17-day Scientology auditing process designed to treat her psychological instability.

Two weeks earlier she had been checked into a psychiatric ward after having been discovered naked and disoriented after a car crash in Clearwater, Florida.

A policeman who attended the scene, identified in court documents only as Officer M Stonewall, described her behaviour as “erratic” and noted that she seemed desperate for help.

“I spoke to the victim about her behaviour. She indicated that she was having a hard time at the church because she was not concentrating,” Officer Stonewall said in a statement.

“She would not go into any further detail about that … I also noticed that as I spoke with her she appeared to be in a daze. I had to ask her the same questions several times to get a response. The victim contributed the accident to her having a lot on her mind.”

When the church found out she was receiving psychiatric care, they sent officials to the hospital to intervene. A short time later, Lisa was discharged and escorted to the church’s nearby headquarters, Flag Land Base.

Tragically she would not leave the building alive.

Over 17 day intense auditing program during which time she lost a reported 20kg while confined to a bed, McPherson went into a catatonic state and died.

A post mortem examination later revealed she had died of a pulmonary embolism.

The church was eventually charged with “abuse and/or neglect of a disabled adult” and “practising medicine without a license” but the charges didn’t stick.

According to the documentary, David Miscavige then spent a reported $US30million fighting a wrongful-death suit brought against the church by McPherson’s family and the case was settled out of court for an undisclosed sum.

The Church has since denied all claims of wrongdoing against McPherson.

Marty Rathbun, a former Scientologist who featured in the documentaries Going Clear and My Scientology Movie, has alleged that church officials destroyed all files related to McPherson’s case.

Meanwhile, Shelly Miscavige, the wife of Church of Scientology supreme leader David Miscavige, has not been seen in public since 2007.

The last people to see Miscavige alive all agree that she vanished in disturbing circumstances.

Members who have dared to question her fate have all since left the church and include Jefferson Hawkins, Scientology’s chief marketing executive of 30 years, Australian Mike Rinder, the church’s former special affairs director, and former executive Tom DeVocht.

Both Rinder and DeVocht feature prominently in Oscar-winning director Alex Gibney’s film adaptation of Lawrence Wright’s book Going Clear: Scientology, Hollywood, and the Prison of Belief.

According to these former devotees, Shelly had expressed concerns in the months leading up to her disappearance in August 2005 (two years before the date stated on official missing persons reports).

Further to those concerns, Shelly took it upon herself to complete several outstanding tasks relating to the organisation structure of SeaOrg, the church’s controversial religious order, which has been described as a brutal boot camp. According to Rinder, Shelly took him aside in 2005.

“I knew that she was in deep s***. That was the last conversation I had with Shelly,” Mr Rinder said.

A week later, Shelly Miscavige vanished.

Months after that conversation, Mr Rinder alleges that he was placed into the church’s camp “The Hole” for more than a year as a prisoner, enduring beatings and torture before finally leaving Scientology during a 2007 trip to London.

In 2013, about eight years after Shelly was last seen, two people filed a missing persons report with the Los Angeles Police Department (LAPD). One of them was Lawrence Wright, the Pulitzer-prize winning journalist and Going Clear author. The other was King of Queens actor and former lifelong Scientologist Leah Remini, who has written a book about her life in the church.

Ms Remini has stated that Shelly’s disappearance was central to her defection and that she started to break away when she didn’t get satisfactory answers to questions about her friend’s whereabouts.

The Church of Scientology described Remini’s actions as “harassment” and “a publicity stunt cooked up by a small band of unemployed fanatics who live on the fringe of the internet”.

“This ill-advised, ludicrous self-promotion and the media inquiries it generated caused an inexcusable distraction for the LAPD. The entire episode was nothing more than a publicity stunt for Ms Remini,” the church said in a statement.

It rejected suggestions Shelly was “missing”, insisting she was alive and well and “working non-stop for the church out of the public eye”.

The LAPD declared the missing persons reports “unfounded” and closed the case after claiming one of its detectives interviewed Mr Miscavige and personally sighted Shelly. However, the officer has never been named and her location never disclosed, leading to accusations of corruption and cover-up. It is well known that the church’s Celebrity Centre holds regular fundraisers for the LAPD.

Journalist, activist and blogger Tony Ortega has written dozens of articles relating to Shelly’s disappearance as part of a relentless campaign to expose alleged abuses by the church.

The former Village Voice editor runs a blog called The Underground Bunker, which features interviews with defectors and whistleblowers as well as satirical content including videos, cartoons and memes.