THE last people to see the Scientology’s first lady Michele “Shelly” Miscavige all agree that she vanished in disturbing circumstances.

Shelly, the wife of Church of Scientology supreme leader David Miscavige, has not been seen in public for more than a decade.

The witnesses who have spoken out about her going missing have all since left the church (of course, otherwise we wouldn’t be hearing from them) 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 members, 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 Scienologist Leah Remini, who has spoken out about the church in a new book.

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.

According to Mr Ortega and others with inside knowledge of the organisation, Shelly is most likely being held against her will at a secret 200ha compound in the LA mountains known as “Twin Peaks”. A 2014 Vanity Fair article quoted “multiple” unnamed sources as describing it as a place “monitored by armed and surrounded by spiked fences” where Shelly had likely endured “months of auditing, reprogramming and menial labour in an effort to instil her with sufficient levels of ‘clarity’ after her perceived insubordination”.

She was allegedly taken there sometime between in August 2005 and 2006.

“The compound is the headquarters for Scientology’s most secretive entity, the Church of Spiritual Technology, where L Ron Hubbard’s works are stored in underground vaults, so they can survive a nuclear holocaust,” Mr Ortega said. “For the past 10 years — except for a couple of days in the summer of 2007 when she was let out to attend the funeral of her father, Barney Barnett — Shelly has been living and working at CST’s headquarters compound.”

Unlike others, Mr Ortega believe Shelly is likely still alive.

“The astounding thing about Shelly is not that she’s missing, because she isn’t,” he said.

“Is Shelly happy working there? Is she being held against her will? Would she take the opportunity to escape if she could?

“We reported in 2013 that Shelly does have some limited communication with the outside world, and was asked by a family member how she might be able to leave the base. ‘There’s only one way,’ she responded, and Mike Rinder told us he interpreted that to mean that only another family funeral would allow Shelly to go outside the confines of the compound.”

It was Mr Ortega who discovered that Shelly’s mother Flo Barnett had died in mysterious circumstances in 1985, four years after her daughter’s marriage to David Miscavige. The incident barely made a ripple at the time because it was overlooked by the media.

Mrs Barnett was found dead with four bullet wounds to her body — including three to the head and one to her chest. The medical examiner ruled her death suicide, claiming she had shot herself with a rifle. Two suicide notes were found and cuts were found on the 52-year-old’s wrists.

What do we make of the fact that a mother and daughter once ranked in the highest tier of the church both suffered so much? And if the truth about Shelly is ever revealed, could it finally be the undoing of this secretive organisation?