It was a saga that started on Memorial Day weekend in 2014 when two already romantic Michigan State University students, referred to in legal documents as Nathan and Melanie, began a consensual sexual tryst in the backseat of a car.

A passerby interrupted them, and Melanie revealed that the incident brought up unpleasant memories of a previous abusive relationship. The incident and its aftermath triggered a long-running and sometimes confusing case that underscores the challenges colleges and universities face in dealing with ambiguous sexual assault allegations outside the legal system.

Later that night, Nathan tried to resume the encounter -- reaching underneath Melanie’s shirt -- but he said he stopped after she rejected him. Sixteen months later, Melanie -- who reportedly is awaiting gender reassignment surgery and now identifies as a man -- made a formal complaint to MSU officials for the “one-time, non-consensual touching.”

Melanie cited being transgender as a key reason for coming forward, and claimed to fear encountering her ex-lover in the male bathrooms.

The complaint came after the school launched a revised sexual-harassment policy, one featuring more explicit definitions of sexual misconduct. Schools across the nation did the same, after the Obama administration threatened to withhold Title IX funding if schools did not crack down on sex assaults.

The case has since led to more than 2 ½ years of administrator investigations, legal bills and sanctions against Nathan – and it is not likely to be closed anytime soon. His attorney, self-titled feminist and progressive Deborah Gordon, said she intends to file a federal lawsuit against MSU on his behalf.

“The so-called sexual harassment is not really sexual harassment. I have been doing these cases for more than 30 years. The breast touch occurred in the summer, off campus, the school was not in session, it had nothing to do with the school,” Gordon told Fox News. “Title IX does not require you to take cases when they don’t involve the school.”

In the firestorm over on-campus rapes during the Obama administration, Gordon said that Nathan fell victim to the get-tough policies that punished the accused even if the evidence against him or her was flimsy. In Gordon's view, his case was one of overzealous school administrators trampling on a student's civil liberties to protect the institution.

Throughout his administration, Obama took a hard line against sexual violence on campus. In 2011, his Department of Education’s Office for Civil Rights sent letters to college administrators across the country requesting tougher and faster enforcement for sexual assault cases, rendering institutions responsible for their dealings with such cases. The letter also threatened non-compliant schools with reduced federal financial support.

The Nathan and Melanie encounter took place prior to the implementation of the new guidelines; however, the gender studies professor tasked with the investigation incorrectly listed on the documents the date of the incident as being after the new guidelines were implemented, and so Nathan was investigated under the updated policy.

Nathan has not been charged with any type of crime by local authorities, but has been punished for sexual harassment by MSU under the Obama administration’s federal Title IX anti-discrimination law. The university’s ruling means it stays on his permanent record and he has to divulge the information when he is seeking employment.

“This is not a rational result. You cannot deprive a student of his right to an education without due process of law. He had no opportunity for a hearing,” Gordon said. “And yet [he] is going to have a permanent record that says he engaged in sexual misconduct and that is a very serious thing. Apply for anything, and you are asked about your disciplinary record.”

To Gordon, this case is nothing short of overkill.

California-based criminal defense attorney Troy Slaten said Nathan’s case underscores how the campus rape scandals eventually led to prosecutorial overreach.

“The ‘investigative model’ that universities are employing pursuant to Title IX deprive students and the public of the benefit of traditional notions of fair play and substantial justice in these quasi-judicial proceedings. Most deprive the student, the accused, of traditional rules of evidence and cross examination,” he explained. “Often the hearing officer is also an advocate for the alleged victim. This is akin to the prosecutor and judge being the same person.”

Slaten said it appears “unconstitutional for a student to suffer permanent and public sanctions without due process,” and that it seems as though the university was “under the microscope by the federal Department of Education and reacted in a way that was disproportionate to the alleged victim.”

MSU did not respond to a request for comment.

Not everyone, though, agrees that the Nathan and Melanie case is an irrational one. Although accurate statistics are difficult to obtain, the National Institute of Justice says that 1 in 5 women have been the victim of rape or attempted rape while in college. Advocates for sexual assault victims stand by MSU’s investigation.

“This is a big deal. Prior consensual sex does not give anyone the right to have sex subsequently without consent. The woman was deeply upset and embarrassed. This is not a state of mind conducive to sexual relations,” said John Foubert, national president of One in Four, a group dedicated to supporting college sexual assault victims. “He has no standing to sue. We have got to learn that women’s bodies – and men’s for that matter – are not open access formations for us to touch at will.”

It is not yet clear what mechanisms the Trump administration will use to combat sexual violence on campus and what changes will be made to the Title IX guidance. Department of Education Secretary Betsy DeVos has said it would be “premature” to commit to standing by the previous administration’s directive.

And even though the Obama team put the issue at the top of its education agenda, Foubert insists that not enough is being done to tackle the epidemic of campus sexual assault.

“I would advise the Trump administration to quickly increase the staff in the Office of Civil Rights in the U.S. Department of Education,” he added. “Too many institutions are trying to come out looking clean when, in fact, they are covering up rape on campuses. They deserve a federal investigation that happens in a reasonable time frame.”