“When I got there, Baylor, a school older than the state of Texas, did not have a single Title IX file,” she said. “There is a group of faculty and administrators who are working very hard to get across that Title IX and diversity initiative are not biblical.”

She eventually quit in disgust, but only after she established protocols and tabulated 417 allegations of sexual assault and harassment over several years, 90 percent of which had nothing to do with athletics.

“It was utterly overwhelming,” she said. “And football was definitely not the worst.”

She said that Mr. Starr was not among those who bridled at a federal role and that he said he wanted the school to comply with laws. But he did not shy from asserting the school’s religious injunctions. He emphasized after he left Baylor that the university’s prohibitions against premarital and gay sex were “Orthodox Christian doctrine” and “those are our values and we do not apologize.”

Baylor is one of many religion-based universities in the United States that navigate such waters, some quite successfully. The practical effect of Baylor’s acceptance of federal regulations, however, proved problematic. Three past and present female students who said they were raped by fellow students all describe a story of abandonment by officials during that time.

One of these women was a nursing student from small-town Texas come to a handsome Christian campus with grand lawns and overarching oaks. Horror came her way freshman year when, she said, she was raped. She went to a university doctor and told him: I have been assaulted and I need an H.I.V. test. “He said, ‘O.K., let’s draw your blood.’ He did not ask if I had reported this and asked nothing about it,” she recalled.

She asked a Baylor lawyer if by reporting her assault she risked expulsion for premarital sex. Maybe, she said he advised, you should remain silent and concentrate on your work.

A top student, her grades plummeted. She went to her professors and said she was raped and asked for a second chance. She said they replied: “Nurses need to be professional and you need to keep your personal life separate from your schooling and professional life.”