FORMER Scientology staffer is breaking her silence about being sexually assaulted 100 times at ages 16 and 17 by the church supervisor she was “ordered” to live with, and then receiving threats and intimidating phone calls when she reported the abuse.

Five years ago, Gabriel Williams, then a 27-year-old chief supervisor at the Church of Scientology in Mountain View, Calif., forced then-16-year-old Jennifer Stewart to have intercourse with him on the first evening she moved in, according to her statements in court records.

After Williams was charged with rape and sodomy with a minor – and later convicted of sexual battery and sodomy – Stewart’s family endured death threats, stalkers and other harassment.

“We want the world to know that when Tom Cruise calls psychiatry a ‘pseudoscience,’ it’s all part of Scientology’s plan to brainwash people,” said Stewart’s husband, Tom Gorman, referring to the actor’s “Today” show interview in June.

Stewart believed that if she went to the police, she would not be able to avoid being sent to a psychiatrist. According to Scientology, psychiatry is a source of evil. Members who see “psychs” or take psychiatric drugs will be declared “SP” – “suppressive person” – and can’t achieve spiritual freedom.

In a related civil suit brought by Stewart against Williams and the church, she recently received as part of the settlement a “generous monetary resolution,” said her attorney. Although the church admitted no wrongdoing, it forked over about $700,000, sources say.

Stewart’s ordeal began in 2000, when she became a supervisor under Williams at the church in the San Francisco area, where she and Gorman were raised as Scientologists. She had come to know Williams as someone who made “lots of overt sexual comments” about women, she says.

Still, she was told by a senior church staffer that the church had “ordered her” to work from 9 a.m. to 9 p.m. and to live with Williams and his fiancée at their San Jose flat, which was closer to the church than her home, making carpooling easier, she says.

“At the time, Williams was a highly regarded member of the church, so the arrangement seemed safe,” said her father, Michael Stewart. According to court documents, the church said it “refutes any ‘order’ by management instructing the victim to stay with” Williams.

After Williams assaulted Stewart the first night, he did so again the next, telling her, “I’ll kill you if you say anything,” according to the police report.

“Williams told me everything that was happening was my fault because I’d been evil in a past life,” said Stewart. “If I told anyone, I’d be sent to a psych and be taken away from my family.”

Only after Gorman became suspicious of bruises on Stewart’s body in May 2001 did she admit what Williams had been doing, he said.

THE next day, Gorman and Stewart told Stewart’s father. Michael Stewart took his family out of the church and hid his daughter. A few days later, he told church authorities what Williams had done.

“A deputy special affairs officer told me not to go to the police,” said the elder Stewart. “If we did, we’d lose Jennifer to child services.”

“The church had no knowledge of the relationship between Williams and Stewart, and upon learning of the allegations and determining that Gabe and Jennifer were indeed having a relationship, Gabe was immediately fired,” said Jeff Quiros, president of the Church of Scientology San Francisco.

Quiros sent The Post several testimonials from acquaintances and colleagues of Stewart and Gorman, which he said would have been entered as evidence in the criminal proceedings had Williams not struck a plea deal that settled the case without trial.

Elliot Abelson, an attorney for Quiros’ church, emphasized that the church never knew about Williams’ behavior, that Williams was fired within a day of them finding out about the allegations, and that there have been no other such cases within the church.

Michael Stewart finally went to the cops on his daughter’s 18th birthday, when the fear of losing her to the state no longer loomed.

More than a year after his last assault on Stewart, Williams was arrested in Florida in 2002 by a San Jose detective, according to the DA in the case.

While Williams was waiting for his criminal case to be heard, Stewart, who married Gorman in 2002 and now lives with his family in San Francisco, filed a civil suit against him and the church.

That was when the threats began, they say. On one occasion, a man phoned Gorman’s father and said, “SPs don’t live long. Your son and his wife, Jennifer, will be dead soon,” according to a police report.

“Who else would use the term ‘SP’?” said the younger Gorman. Such incidents continued up until three months ago, he says.

After doing about eight months in jail, Williams was released last year. Now on probation, he lives in Clearlake Oaks, Calif., with his wife and two kids.

“I paid my debt to society in this matter, and I was not found liable in the civil action,” Williams said through his attorney.