An upstate New York university has taken its free-speech-zone policy, which regulates where students can hold protests, further than most, charging students who last month organized a protest with trespassing.

The conflict between students and administrators at the Rensselaer Polytechnic Institute stems from a two-year debate over who should control the student union. For more than 125 years, the student union, which helps administer student funds to campus organizations and promote a more prosperous student life, has been operated by the students themselves.

In fact, it is, according to the university, one of the few private school student unions in the country that is entirely student-run.

That’s why when RPI President Shirley Ann Jackson first made moves two years ago to try to assert university control over the union, many on campus were opposed. Jackson has argued that she should have final say over who is hired as the union’s director, a position that has been vacant since the university fired the organization’s previous director in December 2015. The board of trustees agrees with the president, arguing that the student union — which now controls a bookstore, fitness facilities, and recreational spaces — has grown tremendously in the past century and now needs more direct university control.

Last month, a group of outraged students opposed to increased university influence planned a demonstration during Homecoming Week, a time during which alumni, donors, and other bigwigs come to campus for events to promote the school.

But the university responded by outright banning protests during homecoming and turning down a formal request to stage a protest. It then erected a literal fence around parts of campus, preventing students from approaching a building where the president would be hosting university donors for an event. University staff also tore down posters promoting a planned protest.

More than 100 students, faculty, and alumni staged a demonstration about changes to the student union anyway. During the October 13 protest, some protesters pierced the makeshift fence and crossed into the no-go zone.

Dan Seel, a student in a joint bachelor’s and master’s program in science and technology studies, has been involved in the fight over the student union since it began. He attended the demonstration and told The Intercept that both campus and city police were present, and a city police officer instructed demonstrators to stay off the grass and sidewalks but otherwise did not ask them to back off.

“That’s the only instruction we ever received as to how to act or where to be,” he said. “No one from the school ever talked to us or told us to back up behind the fence.”

Then, in early November, the university surprised protest organizers Michael Gardner and Bryan Johns by summoning them to a “judicial inquiry” over their behavior. The two students were charged with trespassing, failure to comply, and “operating a business,” a charge that comes from the act of handing out letters on campus related to the student union campaign. It is not yet clear what sanctions, if any, the students face, and a university spokesperson declined to comment on the specifics of the case.

A university review of the incident says the protest leaders were identified based on information from staff who were present, video footage, and a series of online photos and news reports.

Adam Steinbaugh, who works for the campus free-speech group Foundation for Individual Rights in Education, or FIRE, and has been monitoring the case, said the university is exhibiting a double standard on free speech.

“RPI’s desire to find some policy — any policy — to punish students for holding signs outside of a black-tie fundraiser or for distributing a letter is bizarre,” he told The Intercept. “Private institutions can’t promise freedom of speech while cashing the tuition check, then say it can’t be exercised whenever it might contrast with the institution’s promotional efforts.”

The university offered a muted response to The Intercept.

“It would be inappropriate to comment on any individual student’s situation related to the incident on October 13, 2017, in which individuals breached security barriers as part of an unauthorized demonstration which took place on our campus,” said Richie C. Hunter, vice president for strategic communications and external relations at the school.

Hunter’s response appears to be ripped from talking points authored by Dean of Students Travis T. Apgar, which were sent to the Rensselaer Alumni Association and then shared with students.