It's been more than a decade since Shelly Miscavige, the wife of Scientology's revered yet controversial leader David Miscavige, has been seen alive or in public.

The last people to see Shelly alive all agree that she vanished in disturbing circumstances 13 years ago.

Many former members of the highly-secretive church allege Shelly's husband David would be one of the few people to know where his wife, the high Priestess of Scientology, may be.

In a new investigation by 60 Minutes, the current affairs program travelled to the US and to the gates of Scientology's most secure compound to ask, where is Shelly Miscavige?

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The church has previously claimed Ms Miscavige has gone to ground, working for Scientology behind the scenes while her husband runs things publicly.

The Gold Base Compound, the international headquarters of Scientology. Photo / 60 Minutes
The Gold Base Compound, the international headquarters of Scientology. Photo / 60 Minutes

Others, including Ms Miscavige's former friend Leah Remini, fear for her safety.

Ron Miscavige, the father of David and a member of Scientology for 42 years, is terrified for his daughter-in-law.

"Shelly, she'll never be free," Mr Miscavige tells 60 Minutes.

The church, in its response to the programme, said show was passing off "fiction and salacious gossip as truth".

It's alleged Shelly was locked away by her husband more than a decade ago, less than a year after the high-profile wedding of Tom Cruise and Katie Holmes in 2005.

Through tears, Ron admits it would be easy for the church to have done exactly that.

"I know it's difficult to believe, but the worst thing about this is I'm telling you the truth," he said.

"That's the worst goddamn thing that's going on in this interview. This happens. These are pretty bad people, but they don't have a conscience and that lets them do it.

"She has no hope whatsoever of ever getting into the good graces of Dave or going free. None."

Ron left the church in 2012 and was cut off by Scientology — and his entire family — because of it.

"I feel grief-y because look I lost my family. It's like they're dead. They're gone. My two daughters, my grandchildren," he said.

Mike Rinder, an Aussie and Scientology's former special affairs director, said the church has left hundreds of families broken.

"If there's one thing that is the common thread that we see throughout the stories of Scientology it's broken families. It's destroyed families," Rinder tells the program.

The former Scientology member was once one of highest-ranked officials in the church.

He last spoke to Shelly in August 2005. She had expressed concerns to him about the church but a month later, she'd vanished.

Tony Ortega, a long-time critic and former member of Scientology, has spent years investigating the church.

The Scientology reporter claims Shelly's final moment of freedom came in mid-2005, not long after the high priestess reportedly completed admin work without her husband's approval.

"He just blows his stack, and I've got eye witnesses for this," Ortega told 60 Minutes.

"He had the biggest temper tantrum of all time. A week later she vanished."

Leah Remini, who clawed her way out of Scientology in 2013, is worried sick for her friend.

"You can't just do what you want with a human being," Remini told the current affairs program.

Remini filed a missing persons report for Shelly in 2013

The Los Angeles Police Department ruled the report was "unfounded" and closed the case, claiming officers had met with Shelly.

A lawyer representing Ms Miscavige told 60 Minutes the Scientology queen was "disgusted" about Remini's allegations and denied suggestions she was missing.

But Remini is still fighting.

"It's getting boring, this response from Scientology. And I'm gonna say it. I'll say it every time now. Cut the bullshit," she said.

"If what we're saying is untrue, sue us, me and Mike (Rinder). We're ready for the lawsuit, so that's what I keep saying. we welcome your lawsuit. We welcome it."

The moment Leah Remini noticed

As Leah Remini stood with her Scientology friends at the 2006 wedding of Tom Cruise and Katie Holmes, she looked around for her friend Shelly.

David Miscavige, the leader of the highly-secretive church, was there as Cruise's best man.

But his wife Shelly, who he married in 1982, wasn't.

That was the first time Remini, who very publicly left Scientology in 2013, held concerns for her long-time friend.

Leah Remini and Mark Rinder welcome a lawsuit from Scientology. Photo / 60 Minutes
Leah Remini and Mark Rinder welcome a lawsuit from Scientology. Photo / 60 Minutes

"Shelly was always where David Miscavige was," Remini told ABC News in 2015.

"It was a wedding of the century … it was like, "where's Shelly?'

"It's such a simple thing. It's a big wedding that the leader of the Church is here and his wife isn't. It's getting weirder because you're making it weirder," Remini said, claiming anyone she tried to ask wouldn't give her a straight answer.

Nancy Many, who left Scientology in 1996, said Remini was "attacked" when she asked about Shelly's disappearance.

"Leah asked about David's wife and came under an unbelievable torrent of attack on her, an attack and inquisition," Many told Reuters in 2013.

Nine months after Remini questioned the whereabouts of her friend, Shelly made what has remained her final public appearance.

In her December 2016 series Scientology and the Aftermath, Remini said LAPD's response left her with more questions.

"There's still answers that I need. I do not know that she is alive. I do not know that she's not being held against her will," she said.

"I do not know these things and so if the church produces her, by bringing her to an event, even if she went on a program and said, 'Hi, Leah Remini. Go f*** yourself,' I'd be happy to know that she was alive.

"The police department should say, 'Yes, we've seen her.' No, I wasn't told that. I was told that a representative saw her or spoke to her. I'm going to continue to get and gather information."

In a statement released ahead of Remini's eight-part documentary, the church said the actress "seeks publicity by maliciously spreading lies about the Church using the same handful of bitter zealots who were kicked out years ago for chronic dishonesty and corruption and whose false claims the Church refuted years ago, including through judicial decisions".