In 2006, Miscavige returned from a trip aboard the
Freewinds before her husband did. During her husband's absence, she made appointments to the Org Board on her own. After David Miscavige arrived, Shelly was said to have "visibly changed" her mood and to have "looked cowed".
Mike Rinder, then Scientology's chief spokesman, has said that Miscavige asked him if her husband was still wearing his wedding ring. Shortly afterwards, in June 2006, she disappeared and no longer made any appearances in public. Miscavige has not appeared in public since August 2007, when she was spotted being escorted to her father's funeral. At least two
missing person reports have been filed with the
Los Angeles Police Department concerning Miscavige. Author
Lawrence Wright has mentioned one such report, though he did not say who submitted it. Another was filed in August 2013 by actress
Leah Remini; the ensuing investigation was closed within hours by the LAPD and described as "unfounded". The LAPD added that it had "located and spoke[n]" to Shelly Miscavige. As of 2026, the Church of Scientology had not commented on Miscavige's location. Some former Sea Org members have said that they believe Miscavige is being held against her will at the
Twin Peaks compound of Scientology's
Church of Spiritual Technology corporation near the mountain town of
Running Springs in
San Bernardino County, California. In 2011, Lawrence Wright said that Scientology spokesman
Tommy Davis had told him that he knew Miscavige's whereabouts, but would not divulge that information. In July 2012, in response to speculation in the media on Miscavige's whereabouts, lawyers who claimed to represent Miscavige informed two UK newspapers that Miscavige was not missing and that she "devotes her time to the work of the Church of Scientology." In 2017 Miscavige registered to vote from
Petrolia, California. Scientology also has a base in Petrolia where they house CST documents. Remini questioned Miscavige's whereabouts during an episode of
Leah Remini: Scientology and the Aftermath in December 2018. Remini has pushed for an investigation into the conflicts of interest and relationship between the Church of Scientology and the Hollywood Division of the LAPD. There continues to be speculation about Miscavige's whereabouts. In 2025, her niece
Jenna Miscavige Hill stated in an interview that she believes Shelly is alive, working at the Twin Peaks base, and is stuck in a cult.
Popular culture on the disappearance There have been many parodies of Miscavige's disappearance, and the question "Where is Shelly?" has become a
meme. The
Fox police sitcom television series
Brooklyn Nine-Nine makes reference to Miscavige's disappearance in its fifth-season episode "
NutriBoom". The episode satirizes Scientology as a
multi-level marketing company that produces amino acids and amino acid reducers, allegedly to improve their clients' health.
Brooklyn Nine-Nine's parody of Miscavige, Debbie Stovelman, is found to be alive and well, having faked her own disappearance to allow her to run NutriBoom and escape the consequences of illegal activities. In
John Oliver's
Last Week Tonight Miscavige's whereabouts have become a
running gag. In his October 2021 segment on Taiwan, and in the March 19, 2023, segment on
Timeshares Oliver said, "Where's Shelly?" In his April 2023 segment regarding
Mickey Mouse's future lapse into
public domain, an animated Mickey repeatedly asked "Where's Shelly Miscavige?", which Oliver stated would become his
catchphrase. At the
80th Golden Globe Awards in January 2023, host
Jerrod Carmichael joked that since Tom Cruise had returned his three Golden Globe awards the previous year, those trophies could be exchanged "for the safe return of Shelly Miscavige". ==Family tree==