The University of New Mexico president, Robert G. Frank, agreed that universities had a responsibility to maintain an atmosphere free of verbal sexual harassment. But the federal government, he said in an email, “offers no specific guidance” on how to do that “in the real world without infringing on free speech,” especially at universities where “the exchange of controversial or sensitive ideas is woven into the fabric of academe.”

Universities investigated for violations of Title IX, or those that do not adequately investigate charges of sexual assault or harassment, face lengthy and expensive investigations — 246 cases are currently under investigation at 195 campuses. Those found guilty, public or private, could lose federal funding.

Understanding Title IX, Mr. Lukianoff said, “is not sexy and it’s complicated, but it is the secret engine as to why universities overreact” in creating and enforcing speech codes and in charges of harassment or sexual assault. “When people say, ‘Look how crazy our universities have gotten,’ they need to understand that they are being pushed with a very scary threat,” he said. “They’re not just scared of loss of funding. They’re scared of the investigations.” Colleges and universities, he said, are being “asked to do the impossible.”

There are other groups that fight for First Amendment rights on campus, but none as vocal — or pushy — as FIRE, which has gone public with 421 interventions on behalf of aggrieved students and faculty members over almost two decades (many more have been resolved privately).

The organization, which has headquarters in Philadelphia across the street from Independence Hall, has nearly doubled its staff, to 35, in the last two years. In 2015, FIRE received 807 inquiries from students and professors seeking assistance in fighting perceived civil rights violations, up from 719 in 2014. About 50 will fit FIRE’s “narrow focus” on civil liberties defense, said Peter Bonilla, director of its individual rights defense program. The most egregious get litigated through FIRE’s two-year-old litigation program, which targets violations at public colleges (only public institutions, which are arms of the government, are directly bound by the First Amendment).

A lawsuit is FIRE’s tactic of last resort, especially when it comes to speech codes. In about 90 percent of cases, it uses “persuasion,” as staff members call it, to get administrators to revise or revoke questionable parts of a code. Depending on the level of “obstinacy,” Mr. Bonilla said, “the levers of publicity” — news releases, op-eds, media appearances — kick in. Most administrators, wary of bad press or an expensive suit, eliminate the speech codes.

As Mr. Lukianoff likes to note, FIRE has not lost a speech-code legal challenge yet. (He recounts many of them in his 2014 book, “Unlearning Liberty: Campus Censorship and the End of American Debate.”)