The woman, who is being identified as "Jane Doe 1", wrapped up three days of grueling testimony admitting she initially held back information from the Los Angeles Police Department in 2004 claiming she wanted to protect the Church of Scientology and its leader David Miscavige.
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As she shed tears on the stand, the woman said, "I thought maybe I wouldn't get in so much trouble for going to the police. Maybe I could report the crime and keep my family and my life."
"You have to remember that Jane Doe 1 was brought up in Scientology and it's a really totalitarian system," said editor of The Underground Bunker Tony Ortega, who's covering the trial. "You really believe that the Church of Scientology is the most important organization on Earth, and David Miscavige is the most important human being who lives, and a Scientologist would die rather than cause him problems. So even a rape victim, wanting to report the crime to the police, would be thinking, 'Now how do I do this without harming David Miscavige?' It's just incredible."
Jane Doe 1 went on to testify that her Scientology ethics officer Julian Schwartz instructed her to not use the word "rape" in a "knowledge report" she wrote about the alleged rape for the church and later gave to LAPD.
"Jane Doe 1 testified that Julian Schwartz told her that Danny Masterson could not have used a gun in the crime because Danny didn't own a gun. That turned out not to be true," said Ortega. "She said that Julian Swartz also told her to not use the 'R' word in her 2003 document and not to call it a rape because ... they don't do that in Scientology. So, she's describing a situation where she's trying to report what happened, but Scientology is blocking her."
The church said it has "no policy prohibiting or discouraging members from reporting criminal conduct of scientologists, or of anyone, to law enforcement" and that "church policy explicitly demands Scientologists abide by all laws of the land."
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Masterson, 46, has pleaded not guilty to three counts of rape.
The woman, then 27, was the best friend of Masterson's assistant and part of the same social circle of Church of Scientology members.
She testified that she had only intended to go to Masterson's house to pick up a set of keys, and that her relationship had been uneasy with Masterson since the two had sex several months earlier, an incident she told police was consensual in 2004 but later decided she hadn't consented to. She went back to police in 2016.
All three of Masterson's accusers were members of the Church of Scientology at the time they say they were raped, but have since left. Masterson remains a member.
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Judge Charlaine Olmedo said before the trial that she would not allow Scientology to become a de facto defendant, but would allow limited discussion of it.
Masterson's is one of several trials with #MeToo themes going on simultaneously on from coast to coast.
They include Harvey Weinstein's second rape and sexual assault trial just down the hall, and civil trials in New York for actor Kevin Spacey and for screenwriter and director Paul Haggis, who are both being sued for sexual assault.
Scientology also has a major role in the trial of Haggis, a church dissident who is being allowed to argue that the institution is behind the allegations against him.
The Associated Press contributed to this report.