Mary Willingham remembers the exact moment when she realized she had to go public. It was at the memorial service in the fall of 2012 for Bill Friday, the former president of the University of North Carolina. During his long career, Friday had championed the amateur ideal — the notion that college athletes needed also to be students, and that academics mattered as much as wins.

Willingham went to the university in Chapel Hill in 2003 as an academic adviser to the school’s athletes, primarily its football and basketball players. She was a reading specialist, a refugee from corporate America who had become a teacher in midlife. “Mary is one of those people who believed in the mythology, that you can do both athletics and academics,” says Richard Southall, who runs the College Sport Research Institute at the University of South Carolina.

But right from the start, she realized that there was a problem: Many of the athletes were coming into college unequipped to do college-level work. Around 2008, she recalls, after the N.C.A.A. changed its eligibility requirements — depending on their G.P.A.’s, athletes could now get in with lower S.A.T. scores — the situation became dramatically worse.

One way the academic counseling staff kept these athletes eligible was by sending them to so-called paper classes — that is, no-show classes that required one paper (maybe), which would be generously graded. They all took place in the African and Afro-American Studies Department, under the auspices of the department chairman, Julius Nyang’oro.

“The paper classes were incredibly popular,” Willingham told me recently. “But I knew the game would be over at some point, and it was very wrong from an ethical standpoint.”

By 2010, she had moved out of the athletic department — though she remained at the school — and had begun talking on background to a local reporter, Dan Kane of The News & Observer in Raleigh. Building on the information he got from Willingham, Kane broke a series of articles about Nyang’oro’s department. The reports immersed the university in scandal, causing, among other things, Nyang’oro’s hasty retirement. (He has since been indicted.) Mary Willingham, meanwhile, had become a behind-the-scenes whistle-blower.

By the time of Friday’s death in October 2012, the scandal in the African and Afro-American Studies Department had ended. But, in Willingham’s view, the core problem remained: Too many athletes couldn’t do college work. So she decided to go public, giving a series of interviews to Kane in which she alleged that the athletic department resorted to “cheating” to keep athletes eligible.

Once she became an on-the-record whistle-blower, things began to accelerate: In April 2013, she received an integrity award from the Drake Group, which advocates for reform in college athletics. Two months later, she received her first negative performance review and was relocated to a basement office where she was given primarily clerical duties. “They wanted me gone,” she said. (A university spokesman denies that the school created a hostile work environment.)Then, in January, Willingham was the subject of a CNN report in which she alleged that, of 183 North Carolina football and basketball players she had researched since 2005, 60 percent read between the fourth- and eighth-grade levels, and between 8 percent and 10 percent read below the third-grade level. That report set off a firestorm inside the university. At a faculty meeting shortly after the report aired, the school’s provost, James W. Dean Jr., described her data as “a travesty.” (Willingham responds that the provost only looked at one of her data points, and that her assessment derived from, among other things, counseling the students in question.)

“That meeting was like a public trial,” said Jay Smith, a history professor who has been a leading critic of the athletic department. “The purpose was to discredit her.” By this time, it was clear to Willingham that she needed to leave. Her last day at the university is Tuesday.

Willingham is not going quietly, however. The most valuable thing most college athletes can get is an education, she told me, and that’s what they are being deprived of. “I believe athletes should have rights,” she told me, “but an education is the only way out of poverty.”

She also has a reform idea: “If universities are going to continue to admit students who aren’t ready to do the work,” she said, “the N.C.A.A. should pay for 15 months remediation, after which the athlete would have to pass a test.” In addition, she said, they should have five-year scholarships to help improve the odds of graduating.

“I’ve become a reformer,” she said. “I want to see the N.C.A.A. machinery dismantled. I want faculties to take back their universities from the athletic departments. I look at what is going on out there: the O’Bannon lawsuit, the union drive at Northwestern.” She paused. “I think we have a movement here,” said the whistle-blower.