The rotunda on the lawn at the University of Virginia in Charlottesville. (Jay Paul/For The Washington Post)

— The Phi Kappa Psi brothers sat together in a bedroom, turning the glossy magazine pages as they absorbed the account of a gang rape that allegedly took place within the brick walls around them.

The University of Virginia students read the Rolling Stone article that November night in complete surprise. A U-Va. junior said she attended a date party at the fraternity house in 2012 and was lured to a bedroom, where a group of men raped her in what appeared to be a gruesome initiation rite. The students were disgusted, emotional and confused.

“Some people actually had to leave the room while they were reading it because they were so upset,” said Phi Psi President Stephen Scipione, 21, a junior from Richmond.

But within 24 hours of the article’s publication, the U-Va. students reviewed the fraternity’s records and confirmed their initial suspicions: The magazine’s account was deeply flawed.

“We knew that the Rolling Stone story was not true,” said David Fontenot, 22, a senior from McLean, Va. But they also knew “that we would only make things more difficult by fighting it in the media and that our best move was to stay quiet, let the police do their jobs and ride it out until the time was appropriate.”

U-Va. timeline

Phi Psi members, speaking publicly for the first time since the allegations surfaced, told The Washington Post that they went into hiding for weeks after their home was vandalized with spray-painted messages calling them rapists and with bricks thrown through windows. They booked hotel rooms to avoid the swarm of protesters on their front lawn. They watched as their brotherhood was vilified, coming to symbolize the worst episode of collegiate sexual violence against women since the 2006 Duke University lacrosse team scandal — which also turned out to be false.

“That leads back to the bigger problem in that our society tends to rush to judge without the facts,” Scipione said. “They just see the headline and get upset, and they want to blame it on someone, and obviously we were the easiest targets for that.”

Scipione said members of Phi Psi learned about the general allegations in mid-September, when an executive from the fraternity’s national office called an emergency meeting. At the fraternity house, a Phi Psi official outlined what a university official had relayed about the alleged sexual assault.

“He basically asked if, one, we knew about [the allegations] and, two, if we had committed it,” said Scipione. “The look around the table was complete shock and awe.”

Before the story was published, Scipione said he received an e-mail from Sabrina Rubin Erdely, the Rolling Stone reporter, who asked three questions about the rape allegations but offered no specific details, such as the date of the alleged attack. Scipione said only a small part of his response was included in the article.

“More than anything, people wanted to figure out what the truth was,” Fontenot said.

After reading the article, Phi Psi leaders scanned archived e-mails and checked bank statements, determining that the fraternity did not host a party on the weekend of Sept. 28, 2012, the time of the alleged attack. They also determined that no Phi Psi members matched the article’s description of the attackers, calling into question one of the main elements of the account.

Most alarming to the members was the idea that a gang rape could be part of a hazing ritual.

“We vehemently deny that it would be plausible as a ritualistic tradition to join our fraternity,” Scipione said. Fontenot added: “It’s animalistic and totally unrealistic.”

Scipione and Fontenot said that the Phi Psi brothers experienced a difficult fall semester but said no one should consider the fraternity members as “victims.”

“We don’t want to take away from the real victims, which are the victims of sexual assault,” Fontenot said. “We think it is incredibly unfair that the Rolling Stone article could in any way take away their credibility and the support they need.”

Rolling Stone has asked the Columbia Graduate School of Journalism to investigate the handling of the article and has deferred comment until after that inquiry. A Rolling Stone spokesman did not respond to a request for comment Wednesday.

Although the Rolling Stone article was discredited and the student’s account challenged — the magazine apologized for inaccuracies after The Post discovered significant discrepancies in the article — it wasn’t until this week that Phi Psi was officially cleared.

On Monday, the first day of the spring semester, Charlottesville police announced that an investigation found no basis to believe that an attack occurred at the fraternity.

U-Va. also reinstated the fraternity on campus that day, with university President Teresa A. Sullivan issuing a statement: “We welcome Phi Kappa Psi, and we look forward to working with all fraternities and sororities in enhancing and promoting a safe environment for all.”

The Greek system that Phi Psi rejoins is one that has spent the past two months focusing on the issue of sexual assault as a result of the campus turmoil the article created. The university administration suspended all fraternity functions through the first full week of January, affecting about one-third of the school’s 15,000 undergraduates.

Sullivan said last week that she would immediately lift the ban if fraternities signed a new contract with the school that is designed to discourage binge drinking and enhance safety measures at large parties.

Two fraternities — Alpha Tau Omega and Kappa Alpha — said Wednesday they would not sign the contract, arguing that their policies are more stringent than what the university outlined and assailing the decision to suspend the houses.

“At the end of the day, every fraternity and sorority student at U-Va. was punished with a suspension for doing nothing wrong,” said Kevin O’Neill, an attorney for the two fraternities. “The discussion over the need to sign a new [contract] is a process created to distract from the university’s bad decision in suspending our organizations last fall.”

Anthony P. de Bruyn, a spokesman for the university, said in an e-mailed response that “the Greek organizations have until January 16 to sign the new agreements, developed by the student groups themselves, and we will have no further comment or action until that date has passed. We remain hopeful that all groups will commit to these reasonable protocols designed to improve student safety.”

University officials said that Phi Psi was the first fraternity to sign the updated agreements, and Phi Psi leaders said the fraternity has instituted a sexual-assault education and awareness program that is mandatory for new members. Spring rush, an annual recruitment period, is scheduled to begin here Thursday night.

George Elias, a 2013 graduate, said he took pride in the bonds he forged with the 16 other members of his Phi Psi pledge class. He arrived in Charlottesville in 2009, coming from the Philadelphia suburbs as the only senior in his 1,000-student graduating class to enroll at U-Va., and he joined Phi Psi after he was impressed by the brothers.

“I didn’t know anyone in the frat,” said Elias, 24. “They were very accepting of all kinds of people, and they didn’t judge you from your background.”

Elias treasures his years at Phi Psi, but when the Rolling Stone article was published, he found himself doubting the people he knew best. As the fraternity was vilified, Elias said, he hesitated to admit to co-workers that he was a member.

“The day it came out was the most emotionally grueling of my life,” said Elias, who works for a Washington-area construction firm.

He said that members of the fraternity began analyzing the article and quickly challenged troublesome assertions, including that the alleged gang rape was part of a hazing ritual at Phi Psi.

“That ritual part hit hard for everyone,” said Elias, who lived in the Phi Psi house his junior and senior years, including in fall 2012, when the attack was alleged to have occurred. “It assumes that everyone that is part of the frat had to do that, and that hurt a lot of us.”

Scipione and Fontenot said that the ordeal, while a challenge, brought members of the house closer together. They said that despite the inconsistencies in the Rolling Stone story, the fraternity members hope that sexual assault remains an important topic of discussion at colleges across the country.

“Sexual assault on college campuses is a real problem, and it needs to be addressed. And just because one story from Rolling Stone dropped the ball doesn’t mean we can dismiss it,” Fontenot said.

“My worst nightmare from this is someone at this school or anywhere else tells their friends that they’ve been sexually assaulted and their friend on the other line says, ‘Are you pulling a Rolling Stone on me?’ ”

Susan Svrluga in Washington contributed to this report.