Several days later the magazine's editors received an email from the reporter with the subject line "our worst nightmare".
"We're going to have to run a retraction," wrote Sabrina Rubin Erdely about her now-discredited story, "A Rape on Campus".
The message is among hundreds of pages of notes, emails and other documents released on Friday that shed light on the reporting and fallout of the piece.
The documents were made public through a lawsuit filed by Nicole Eramo, an associate dean of students at the university who had counselled "Jackie," the woman who claimed to have been raped. Eramo sued Erdely and Rolling Stone for US$7.5 million, arguing that the story cast her as the "chief villain".
The story horrified university leaders, sparked protests at the school and prompted a new round of national discussions about sexual assault on US campuses.
But an investigation by Charlottesville police found no evidence to back up Jackie's claims and details in the lengthy narrative did not hold up under scrutiny by other media organisations.
Rolling Stone officially retracted the story in April 2015, and the magazine's managing editor and Erdely both apologised.
The documents reveal inconsistencies with Jackie's story, whose last name is redacted in court documents, and missteps by Erdely, who said she found no reason to believe Jackie wasn't credible throughout her reporting.
For example, Erdely said according to a transcript of her deposition that she was aware that Jackie had initially told her roommate she was attacked by five men, but later said it was actually seven men.
Erdely also noted at one point that Jackie's mother's profile on Facebook said she herself went to Providence College, even though Jackie said her mom went to Brown. When asked in her deposition whether that raised any red flags about Jackie's credibility, Erdely said "it didn't seem to be all that important".
Jackie said she had scars on her back from the attack, but her boyfriend said he had never seen them, Erdely's notes say. Erdely said in her deposition that she made a mental note to bring it up with Jackie's mother, but ended up never speaking to her.
Erdely went back to Jackie after other reporters started raising questions about the accuracy of the story, according to the documents. She talked to Jackie early on the morning of December 5 and when she asked for help in finding her attackers, "it spiralled into confusion," Erdely's notes say.
"By the time we ended our conversation, I felt nearly certain that she was not being truthful," according to Erdely's notes. "Then I called her friend Alex, who has been a valuable resource; and I found out that over the past day, Alex has also come to the conclusion that Jackie has probably been lying," she wrote.
In her deposition, Erdely called it the "most devastating moment" of her career.
Libby Locke, an attorney for Eramo, said in an email on Sunday that Erdely knew Jackie's story changed materially over time and published the "false and defamatory article despite serious red flags and without any real due diligence".
Attorneys for Jackie and Erdely didn't immediately respond to messages seeking comment on Sunday.
"Having discovered, in the early morning hours, that the person who I had absolutely believed and trusted had, for whatever reason, turned out not to be credible," Erdely said in her deposition. "And I didn't know whether what we had published was truthful or not."
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