In HBO's explosive new Scientology documentary "Going Clear," one of the most interesting and least discussed allegations is how Scientology once hand-picked and groomed a young church member to become Tom Cruise's girlfriend.

As former Scientologists explain in the documentary, the church does whatever it can to keep Cruise happy because "In the eyes of [Scientology leader] David Miscavige, Tom Cruise is the perfect Scientology celebrity," according to ex-Scientology executive Mike Rinder.

The church reportedly kept Cruise happy by doing him favors like tricking out all of his cars and motorcycles.

And decking out his airplane hanger in Santa Monica, California.

So when Cruise was looking for a new girlfriend after his breakup with Nicole Kidman, the church jumped to help, the documentary said.

"Tom was in Spain. They were opening a new Scientology church in Madrid, and he was overheard complaining that he needed a new girlfriend," said Lawrence Wright, author of best-selling book "Going Clear" on which the documentary is based. 

"Soon after that," Wright said, "a young Scientologist pre-med student named Nazanin Boniadi was told she was going to get a special assignment."

At this point in the documentary, director Alex Gibney chimed in via narration to explain: "Years later, Nazanin became a successful TV actress..."

"... and would have a small part in a Paul Haggis [director and former Scientologist] film."

"But at the time, she was a dedicated young Scientologist..."

"... who believed in the church's claims for its humanitarianism mission."

"In fact, she set a monthly record for selling books for the church."

"Nazanin may not speak publicly about her experiences because of an NDA the church pressured her to sign," Gibney said, "but I discovered details from FBI testimony regarding her ordeal."

"David Miscavige assigned Nazanin's case to a key church official, Greg Wilhere," Gibney said. "He put her through a one-month program of on-camera interviews, intensive auditing, and some security checks."

"She was moved into the Celebrity Center, separated from her family, and certain problems were addressed during this period of time," adds author Lawrence Wright. "One was that she had a boyfriend."

"She is handed a transcript of his auditing session in which he admitted that he had an affair," Wright said, "so she broke up with him."

Now that Boniadi was single, it was time for her makeover.  

"Wilhere took her to an orthodontist to have her braces removed," Gibney said.

"At Burberry and other stores in Beverly Hills, he bought her $20,000 worth of clothes."

"At the Celebrity Center, a man who worked for Cruise's hairstylist colored Nazanin's hair to Cruise's liking."

"Nazanin was told that her makeover was part of the church's humanitarian mission, because she had to look her best for conferences with world leaders."

"Only after she was flown first class to New York, did she discover the actual role that the church wanted her to play — she was to be the girlfriend of Scientology's biggest star."

"Within a month, Nazanin was living with Cruise. While at his house in Telluride, Miscavige came to visit."

"Overcome by a severe headache, Nazanin had a hard time understanding Miscavige, which infuriated him. The next day, Cruise — inches from her face — pounded on the table and screamed at her for insulting the head of the church."

"Two weeks later, church henchman Tommy Davis delivered the news to Nazain that her relationship with Cruise was over."

Director and outspoken former Scientologist Paul Haggis explained what allegedly happened next: "According to her [Bodiani], they [the church] came to her apartment with her mum and found every photograph of the two of them together [Bodiani and Cruise] and took them away and every scrap, every letter, everything, they tossed as if it never existed."

"And she was really upset because she was really hurt by the whole thing. And she made the mistake of telling her friend, who immediately went to tell someone in the church. She agreed to do punishment, like cleaning out the public bathroom on her hands and knees with a toothbrush, while other people she knew were stepping over her.

She did nothing wrong, other than tell her friend she was heartbroken, and this is the way she was treated?"

After the incident, Bodiani pursued an acting career and has since appeared in "Homeland," "Scandal, "How I Met Your Mother," "Iron Man," among many other titles.

Neither she nor Cruise have ever publicly discussed their alleged relationship.

Despite Bodiani's story, "The church claims [leader] Miscavige has no involvement in Cruise's personal life and that the search for Cruise's girlfriend never existed," Gibney states in the film.

But Cruise and Miscavige's relationship is deep, going back decades.

"Tom cruise was the guy," former Scientology exec Mike Rinder said. "Miscavige and Cruise have been pretty buddy-buddy way back to 1990s 'Days of Thunder.' In the eyes of Miscavige, Tom Cruise is the perfect Scientology celebrity."

And it seems like Cruise also enjoys Miscavige's friendship.

In one clip during "Going Clear," Cruise enthusiastically congratulates the Scientology leader during a church conference by proclaiming, "We are lucky to have you. Thank you."

Nazanin Boniadi's rep declined to comment on the story, and Cruise's rep hasn't responded to our request for comment.

Read Scientology's lengthy response to "Going Clear" here.

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