Jane said she was drunk and doesn't remember exactly what happened that night. Jane has said that the next morning, John tried to touch her vagina when she repeatedly told him to stop. Later that night, they had sex again.

Those two days of sexual activities would eventually lead to a major lawsuit against UC San Diego. There are more than 20 other suits which are challenging the way universities handle student claims of sexual assault.

Colleges and universities across the country are required by federal law to investigate and adjudicate whenever a student makes allegations of sexual misconduct.

The procedures vary widely. Most schools hold disciplinary hearings, often made up of teachers and students, some with little training, acting as prosecutor, judge and jury.

And though the punishment isn't as severe as in criminal cases, it's significant for both the accuser and the accused. It can end a college education, and critics of the process say it can unfairly damage lives.

'I tried to object'

Months after the sexual encounters took place, Jane Roe filed a complaint with school officials at UCSD, accusing John Doe of sexual misconduct when he touched her the following morning.

Doe said all their sex acts were consensual and said he had text messages to prove it.

He was investigated and tried by his own university. The tribunal found Doe responsible for violating the school's policy on sexual misconduct for trying to digitally penetrate the woman the morning after they had sex.

But Doe says the hearing was one-sided and unfair. He was allowed to have a lawyer, but the lawyer couldn't speak.

He submitted questions for his accuser, but not all of them were asked. He wasn't allowed to dispute the testimony or examine the evidence.

"I tried to object a few times," he told CNN, "and they reminded me that it was just a school hearing and it wasn't criminal so I wasn't allowed to do that." Doe declined to testify on his own behalf during the proceedings on the advice of of his attorney.

He was suspended from school for one semester, and each time he appealed, his punishment was increased without explanation until he was facing a suspension of more than a year.

"I'm all for true victims of rape to receive all the assistance they need," Doe says, "but at the same time the accused students have rights."

So he sued UCSD, and a state judge agreed with him, finding the tribunal process was skewed and violated John Doe's rights.

Why Title IX is involved

The San Diego lawsuit is one of more than 20 such cases filed against universities in recent years. And what's happening at these disciplinary hearings is coming under increased scrutiny as judges across the country are overturning university decisions that punish men who are accused of sexual assault.

"I don't think the school has any place adjudicating things like rape," John Doe says. "They don't do it with murder or kidnap, so why are they doing it with something just as hard to evaluate?"

The reason is Title IX, a law barring gender discrimination in education.

The Department of Education interprets Title IX to say that sexual harassment is a form of sex discrimination, and therefore schools could be held responsible if they don't investigate and adjudicate these cases.

For years, it was the accusers, not the accused, who complained about an unfair process. Alison Kiss, who runs the Clery Center for Security on Campus, says that it was -- and still is -- common to see outside influences, like high-paying donors or athletics, get in the way of the process.

The criminal justice system is not always an option for these victims, Kiss says, because often these are "he said, she said" situations, where alcohol is involved and too much time has passed for police to have enough evidence to prosecute. In addition, criminal cases take a long time to prosecute, leaving victims feeling vulnerable about running into the people who they say assaulted them on campus.

'Dear Colleague'

In 2011, the Department of Education sent a strongly worded letter to schools, known as the "Dear Colleague" letter, urging them to crack down on sexual assault, calling the statistics "deeply troubling" and providing guidelines for conduct boards.

That meant tribunals used to dealing with issues like cheating and plagiarism suddenly began delving into the complex issues of sexual assault. But the burden of proof is much lower in a tribunal; unlike criminal cases, where charges have to be proven beyond a reasonable doubt, the university panels only need to say it's "more likely than not" that the accused is responsible.

The president of the University of California system, Janet Napolitano, recently wrote about university frustrations over the mandate and the obstacles of the campus hearings.

In the journal Yale Law and Policy Review, she wrote that schools "were left with significant uncertainty and confusion about how to appropriately comply after they were implemented."

Because the Department of Education's guidelines aren't uniform rules, schools are left to come up with their own procedures.

Over-compliance?

"The schools, upon receipt of the Dear Colleague letter and looking at its requirements, weren't completely sure of exactly how to comply, and so in many cases they did more than they necessarily needed to do," says Jeannie Suk, a Harvard Law professor and outspoken critic of the campus tribunals. "They kind of in a sense over-complied. Now, they bent over backwards, and then that's when they put in place -- kind of in a hurry -- these procedures that now don't respect fair process."

Even advocates of the process, like Kiss, say many universities aren't handling this the right way. Schools were so eager to reverse years of mistreatment of victims, she said, that some put procedures into place that led to an unfair process.

"There are some folks that may argue that a hearing has to be victim-centered, and my tenure as a victim advocate and I can tell you absolutely not, we do not want to see these hearings as victim-centered," Kiss says. "We want to see them informed by trauma, and understand the dynamics that some of these crimes have. But they certainly have to be a hearing that's fair and that's impartial."

A prosecutor in flip-flops

Part of the problem, she says, is that universities aren't putting in the time or money to properly train people to handle such a sensitive and complex topic.

From campus to campus, the process varies. Some have students on the panels, some don't. Some allow victims to have lawyers, some don't. Some allow cross-examination, some don't. In some places, those involved watch a PowerPoint. The setting can be casual. In San Diego, John Doe remembered the prosecutor at the UCSD hearing wearing flip-flops.

This year, a new federal law allows for the accused to have a lawyer present, although there is still no guarantee the lawyer can speak.

When Harvard University put guidelines for its tribunals in place, faculty at Harvard Law School rebelled. Suk says she was so alarmed by the lack of a fair process -- she says there was no right to a hearing or for an attorney to participate, and no independent appeal process -- that she and more than a dozen of her law school colleagues wrote an open letter to the Boston Globe in 2014, and then lobbied for Harvard Law to use an independent, law-enforcement-trained investigator, to have an independent appeal process, and to have lawyers on both sides -- even paying for them if the students can't afford them.

"When you have unfair procedures it delegitimizes the process, it makes the whole process seem like a joke. And people don't actually believe in the accuracy of the result when the process itself is unfair," Suk said.

Questionable practices

These disciplinary boards draw criticism from accusers as well. They often feel the university is insensitive.

Eva, who was a student at Southern Illinois University in 2014, says she was sexually assaulted by a fellow student, and the university handled it so badly, she says the process was devastating.

CNN is not using her last name at her request and in keeping with a policy not to identify victims of sexual abuse.

Eva confided in a friend about her assault, and the friend reported it to the university. She says she was shocked when she received an email saying there would be an investigation.

She and the man she accused were both sent an email at the same time, she says.

"The whole reason I didn't report anything was so I could get my education and I could feel safe. And I knew all of that was gone," she said.

The Department of Education says that schools are required to investigate even when victims aren't willing to do so.

Once the process started, Eva says, she had to constantly call the university for updates. "They just ignored my calls, they didn't respond, when they did they were not helpful," she says.

'A semester of torture'

Southern Illinois University would not comment on Eva's case, citing legal and privacy concerns. "The university takes all reports and investigations of sexual misconduct very seriously," Southern Illinois University told CNN.

Southern Illinois University later found the male student responsible and suspended him for two years, but he appealed and he won.

It turned out the university had the wrong date from the friend who reported Eva's alleged assault, according to documents provided to CNN.

Eva says she tried to correct the record the day of the hearing, but no one at the university listened.

The actual date of the alleged assault fell outside the university's own statute of limitations.

So after being dragged through a process she says she never wanted in the first place, Eva watched as her case fell apart because of a procedural error.

"I felt like I had survived a semester of torture, of being forced to relive what was the worst day of my life over and over again, and I felt like it was for nothing," she said.

The Department of Education Office of Civil Rights is investigating Eva's university, along with about 100 others where there are Title IX complaints and the Department of Education found possible violations.