There are a lot of reasons victims of sexual assault choose not to report it. High on that list is fear of retaliation, so many victims won't come forward unless they can stay anonymous.

The criminal justice system cannot guarantee that kind of confidentiality for accusers and the accused. Further, when sexual assault is reported to law enforcement, a majority of cases never make it to trial. In fact, only 3 percent to 18 percent of sexual assaults lead to a conviction, according to research funded by the Justice Department.

But a court case involving the University of Kentucky has highlighted how confidentiality can complicate justice.

Jane Does on campus

Student victims have the option of reporting sexual assault to their school's Title IX office. Title IX is the federal law that prohibits gender discrimination on campus. These offices are also tasked with investigating allegations of sexual misconduct and these investigations come with the advantage of guaranteed anonymity for both the accusers and the accused.

The two women at the center of this case were graduate students in the University of Kentucky Entomology Department when they said their adviser sexually assaulted them. NPR spoke with both women as well as the accused. Because this story is meant to focus on the system, we're respecting the confidentiality of the accused and the accuser. We'll refer to the women as Jane Doe 1 and Jane Doe 2, and the accused as the professor.

NPR obtained a report prepared by the University of Kentucky's Title IX office in which the Jane Does allege the professor groped them and said sexually suggestive things to them while attending separate conferences with him.

The Jane Does told NPR that confidentiality was the most important thing for them when they decided to go to the university's Title IX office with their allegations.

Jane Doe 2 said they never wanted to go through the courts because they couldn't afford to be named.

"I just spent a good portion of my life in grad school trying to further my career and if I'm labeled as someone who filed a sexual assault claim against a professor, that could very easily backfire against me," Jane Doe 2 says. "There's a lot of people in academia who think that there are women who make up stuff like this."

Jane Doe 2's concerns about retaliation in her professional life is just one of many reasons victims of sexual assault choose not to come forward. Research shows that only about 35 percent of rape or sexual assault cases are reported. On college campuses, the percentage of incidents that go unreported is more than 90 percent, according to the National Sexual Violence Research Center.

The Title IX office launched an investigation and after months of interviewing dozens of people and collecting all sorts of evidence, they found enough of it to move to the next step: an official hearing. Who presides over Title IX hearings can vary from school to school, but they are typically run by school officials and do not involve law enforcement. If those presiding over the hearing found the professor guilty, everything would go on his employment record.

But that hearing never took place because the professor was allowed to resign, highlighting what Jane Doe 2 calls a loophole in the Title IX system.

"Not just at UK but at every single university, if a professor resigns before there's a hearing then he's allowed to move on to another university potentially victimizing more students," she says.

In a statement to NPR, the professor said there is no truth to the allegations and that he resigned to protect his family from the publicity and stress of a hearing.

Seeking justice

This gets to the heart of why letting universities handle sexual assault investigations can be problematic. You can't remain anonymous in a criminal case as the Constitution guarantees the right to face our accusers.

It's different going through a university Title IX office, where the primary focus is protecting accusers. The office keeps their identities confidential and there's even a different burden of proof.

Frustrated that there would never be an official hearing, the Jane Does reached out to the university's independent student newspaper, The Kentucky Kernel.

Marjorie Kirk was the first person at the paper to hear the women's story. Kirk is a journalism student at the school who had made a name for herself as an investigative reporter.

"It was March and a person walked in asking for someone to talk to and I said, 'I can talk' and they basically unloaded this huge story on me," Kirk says.

After hearing the Jane Does' story, Kirk was troubled by the lack of transparency on the university's part and wanted to dig deeper.

"I felt an obligation to the safety of other people to try and report this," says Kirk. "And that's why we started this battle for open records."

The newspaper filed two Freedom of Information Act requests seeking all the documents related to the investigation. The university turned over some records, but not all of them citing a law called the Federal Education Rights and Privacy Act — or FERPA, which protects the privacy of student records at all public schools and universities.

"And this institution, the University of Kentucky, has consistently held that student information, particularly in cases that might identifying a student in a sexual assault, sexual misconduct case, must be held confidential," says Jay Blanton, a spokesman for the university.

So the newspaper appealed to the Kentucky attorney general, who sided with the newspaper.

But the university still wouldn't give up the records and because of a quirk in Kentucky law that says the attorney general cannot be named as a party in a lawsuit, the University of Kentucky took its own student newspaper to court in order to block the documents from being released.

For Kirk, the move was reinvigorating. She really did believe the university could have simply redacted names and other identifying details and now she'd get to prove it in court. This time a lot more was at stake than just one professor leaving campus without a hearing.

"A decision would be for all the marbles," said Kirk. "It would affect any decision that a judge anywhere would try to come up with for similar documents. They would see this decision and likely follow the precedent."

Then just two days after the lawsuit was filed, representatives of the Jane Does showed up at Kirk's office at The Kernel and handed over the full investigation. In the more than 100 pages were interviews with witnesses and e-mails where one of the women confronted the professor about his behavior. The investigation also included the professor's version of events.

So Kirk began writing.

She'd publish her first story after receiving the documents on Aug. 13, but the investigation didn't stop there.

"And as we dug into the system a little more, we saw there was much more to this than one professor," she says. "And so the scope definitely grew into a system that universities were enabling."

Pushing forward, pulling back

While Marjorie Kirk was on a crusade, the Jane Does watched with growing concern. They were happy with the first few articles. The women got to maintain their anonymity and the professor was named. But then their personal story mushroomed into something they hadn't signed on for: dozens of articles and an open records fight.

In an effort to put a spotlight on one broken system, the Jane Does stumbled upon another.

Trial-by-Media can be successful in exposing wrong-doing. But media outlets ultimately have say on how they pursue stories and aren't subject to the same rules as the court or universities. So it's really not surprising that The Kernel took the story and tried to expose as much as they could.

In November, the women filed a brief actually taking the University of Kentucky's side.

"There needs to be some sort of reporting system for professors accused of sexual misconduct while still protecting the privacy of victims like me and Jane Doe 1," says Jane Doe 2. "And the records that Marjorie is calling for, those hundreds of pages of documents aren't necessary for that reporting system."

Judge Thomas Clark of the Fayette County Circuit Court tells NPR he plans to issue an opinion sometime in the next two weeks.

But in the meantime, we still have a university struggling to protect students and hold employees accountable, a crusading journalist sued by her own school and two women still searching for a more perfect form of justice.

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