On May 10, 2017, American journalist Tony Ortega reported on FBI testimony that Boniadi had given in January 2010 regarding her brief relationship with actor Tom Cruise from late 2004 until early 2005 through the Church of Scientology. Boniadi's testimony describes how the church's Office of Special Affairs selected her to be Cruise's girlfriend. In October 2004, Nazanin Boniadi was volunteering for the Office of Special Affairs in Los Angeles, then was told by church official Greg Wilhere that she had been selected for a special project. Boniadi was told that her dental braces had to be removed and that her red hair highlights had to be corrected to one all-over colour. She was also encouraged to end her relationship with her longtime boyfriend. Boniadi had to sign a confidentiality agreement, stating she could not abandon this special project without the church's approval. Approximately one month later, after the church arranged for her to fly to New York, she learned that the project was to be a suitable girlfriend for Cruise. Portions of Boniadi's testimony read that "at the beginning of the relationship [he] was very romantic but as the relationship progressed [Cruise] began to have temper tantrums. [Cruise] began to show violent tendencies". In January 2005, after their relationship ended, Boniadi confessed her devastation over the matter to her friend (a fellow church member). She was reportedly punished for this by Church of Scientology's policies. She reportedly "had to dig ditches at midnight and scrub floor tiles ... She was placed on a curfew... escorted everywhere she went". Her testimony also refers to her "feel[ing] she was a victim of white slavery because she traveled across state lines under false pretences".
In 2017, she tweeted congratulations to Leah Remini and Mike Rinder on their series Scientology and the Aftermath winning an Emmy Award. In an interview with the Los Angeles Times Boniadi described her role in Counterpart as cathartic and therapeutic, saying "sometimes there are personal traumas that you don't ever talk about publicly but you pour it into your work". She continued: "this idea of shedding indoctrination and finding out who you are for me is a strong one. It has been extremely therapeutic for me to be able to put it out into the world through my art as opposed to openly discussing it."
