COLORADO SPRINGS, Colo. — Eric Thomas was a third-string linebacker at the U.S. Air Force Academy who also played a far more secretive role on campus: He was a confidential informant, one of dozens of student spies assigned by the academy in the past decade to investigate drug use and sexual misconduct.
Working with an Air Force criminal investigator in 2011 and 2012, Mr. Thomas attended parties where drugs were dispensed and secretly recorded conversations with people suspected of rape. His tips led to three sexual assault convictions in 2013, the first at the academy in more than 15 years, Air Force records show. Those records also suggest that his work was used to begin more than 20 drug investigations.
But the Air Force shut the program down in late 2012 after news reports revealed its existence and prompted angry reactions from alumni. The investigator who had managed Mr. Thomas was transferred to a job emptying trash cans and vacuuming offices, and Mr. Thomas was expelled for misconduct after the Air Force disavowed his undercover work.
Now, his actions are again roiling the academy. Last week, the academy’s superintendent, Lt. Gen. Michelle D. Johnson, said she had opened an investigation into misconduct among student athletes and possible cover-ups by members of the athletic staff, after two Colorado newspapers reported allegations of rape, drug use and spiked drinks at illicit parties involving football players. Almost all of the cases were first reported by Mr. Thomas.
Gen. Johnson pointed to steps the academy was taking to combat such behavior, including awareness and prevention campaigns. But her announcement raised anew a question posed by Mr. Thomas and others: Should the academy reinstate the informant system?
“It worked,” Mr. Thomas, 25, who has been trying for a year to appeal his expulsion, said in a recent interview. “Why would you end the program like that and then go after the two people at the middle of it?”
A spokesman for the academy said it had no student informants now. But in an email Thursday, Gen. Johnson said administrators would consider using informants again if they suspected a crime had been committed or was about to be committed.
Gen. Johnson added that she thought the best approach was “to build trust.”
“We are focusing on personal accountability and accountability to each other so that everyone has the courage to stop misconduct, from minor infractions to major mistakes and crimes,” she said.
In many ways, the academy’s struggle with sexual assault echoes larger problems on college campuses. The crimes usually occur behind closed doors, amid alcohol and drug use that can make memories unreliable. And only about 10 percent of cases lead to convictions, which may discourage victims from reporting crimes.
But the academy is not most colleges. It has federal agents on campus, and students are active-duty members of the Air Force living under strict military rules. Though there are no known cases of other colleges’ using informants — even other military academies say they do not — they are standard in the Air Force, which relies on informants around the world to watch for theft, graft, drugs and terrorist threats.
Defending the practice, a retired deputy judge advocate general for the Air Force, Maj. Gen. Steven J. Lepper, said in a report released in the spring that the academy’s honor code sometimes had to be broken to expose crimes like drug dealing and sexual assault.
But the idea of having students spy on one another is controversial, with both alumni and experts on campus sexual assault arguing that it violates the honor code’s ban on lying and erodes trust among cadets.
“Saying this works is a tricky assertion,” said Alexandra Natapoff, a professor at Loyola Law School in Los Angeles who studies the use of informants in law enforcement. “Does it work to get incriminating information? Absolutely. But does it maintain the integrity of an institution like the academy? Maybe not.”
Mr. Thomas’ work on sexual assault cases began in the fall of 2011, when Sgt. Brandon Enos — an agent assigned to the Air Force Office of Special Investigations, known as OSI — began working at the academy.
Sgt. Enos declined to comment, saying his OSI detachment commander, Lt. Col. Vasaga Tilo, had ordered him not to speak to the news media or the academy’s leadership about the program. But in a 12-page letter sent to members of Congress in May, he said his first case at the academy had involved a female cadet who had been sexually assaulted. She told Sgt. Enos that her attacker had also assaulted other women. But, he recalled her saying, there was nothing the sergeant could do because the cadet was on the football team, which meant he could “get away with murder.”
“I felt sick to my stomach that someone could think this way,” Sgt. Enos wrote in the letter, a copy of which was obtained by The New York Times. “I told the female cadet I would do everything I could to change this culture.”
He decided to try using an informant and, within weeks, recruited Mr. Thomas.
Sgt. Enos directed Mr. Thomas to go after the football team, believed to be a hotbed of misconduct. Thomas began hanging out with the beer drinkers at parties, taking photos on his phone and sometimes wearing recording devices. He met Enos almost daily behind the academy’s B-52 bomber to file secret reports.
“Eric Thomas was how I found out what was truly going on inside the football team,” the sergeant wrote.
In January 2012, based primarily on Mr. Thomas’ findings, the Office of Special Investigations began its largest law enforcement action ever at the academy, interrogating 50 cadets in one day, most of them football players. It called the crackdown Operation Gridiron, records show. Officials at OSI headquarters in Virginia, the academy superintendent and the secretary of the Air Force were briefed regularly, Sgt. Enos wrote in his letter.
Based in part on the work of Thomas and other informants, three football players were convicted in 2013 of sexual assault, including a star linebacker, Jamil Cooks, Sgt. Enos said. Other players were expelled for drug use.
In the wake of those convictions, reports of sexual assault at the academy — a statistic that Air Force leaders regularly cite as a barometer of confidence in the system — almost doubled. This year, after the informant program ended with no further convictions, reports fell by half, according to academy officials.
As Operation Gridiron ensnared more and more football players, it drew the scrutiny of top commanders, who began to push back against investigations of members of the football team, Enos said.
In his letter to Congress, Sgt. Enos said Lt. Gen. Michael C. Gould, the superintendent in 2012 and 2013 and a former quarterback on the team, had repeatedly interfered in cases.
In an interview, Gen. Gould, now retired, called the suggestion that he had interfered with the investigation “preposterous,” citing the academy’s willingness to punish several players last year.
In the spring of 2013, Mr. Thomas was expelled after being caught repeatedly sneaking off base to go to parties and spending time in the presence of underage drinking. Mr. Thomas says those actions occurred largely under the direction of OSI agents. But when he tried to get the OSI to help him, he said, it did not respond.
Mr. Enos said in his letter to Congress that he had been ordered not to speak to the academy on Mr. Thomas’ behalf, and that OSI officials refused to release documents describing Mr. Thomas’ undercover work.
Sgt. Enos was transferred from the academy, stripped of his badge, given menial jobs and told by a commander that he would be kicked out of the Air Force, he said in his letter. He fought his dismissal and is now in the final stages of a medical discharge, his lawyer said.