Republican presidential nominee Donald Trump listens as Democratic nominee Hillary Clinton answers a question from the audience at a debate at Washington University in St. Louis on Oct. 9. (Rick Wilking/Reuters)

Then-New York Times Public Editor Margaret Sullivan called it a “mess.” Rep. Elijah Cummings (Md.), ranking Democrat on the House Oversight Committee, said, “This is the latest example in a series of inaccurate leaks to generate false front-page headlines — only to be corrected later.” “The New York Times Needs to do a Better Job of Explaining Its Epic Hillary Clinton Screw-Up,” read a headline at Mother Jones.

They were all describing one of the highest-profile media kerfuffles of the 2016 presidential campaign. On July 23, 2015, New York Times reporters Michael S. Schmidt and Matt Apuzzo reported that two inspectors general in the U.S. government had requested a Justice Department criminal investigation “into whether Hillary Rodham Clinton mishandled sensitive government information on a private email account she used as secretary of state.”

At least, that’s what the story said before a wave of ferocious objections — starting with the Clinton campaign — prompted the newspaper to amend it. Too slowly for its most motivated critics, the New York Times issued two corrections and an editor’s note. One of the corrections noted that the request didn’t specifically target Hillary Clinton. The other pointed out that there was a problem in how the request was characterized. “It was a ‘security referral,’ pertaining to possible mishandling of classified information, officials said, not a ‘criminal referral,’ ” reads one of the corrections. The editor’s note expressed the newspaper’s regret that the corrections hadn’t been published earlier in the process.

Newly unsealed court documents revealed that the FBI told a federal judge that it needed to search a computer belonging to former congressman Anthony Weiner to continue an investigation of Hillary Clinton's use of a private email server. (Peter Stevenson,Victoria Walker/The Washington Post)

The revisions didn’t satisfy the Clinton campaign. On July 28, campaign communications director Jennifer Palmieri sent a long letter to the newspaper expressing the campaign’s dismay over the story. “I feel obliged to put into context just how egregious an error this story was,” wrote Palmieri. “The New York Times is arguably the most important news outlet in the world and it rushed to put an erroneous story on the front page charging that a major candidate for President of the United States was the target of a criminal referral to federal law enforcement.”

The beatdowns came with clubs. “Flimsy report“; “The New York Times’ Botched Story on Hillary Clinton“; “Another shoddy Clinton smear: Anatomy of the New York Times’ epic email screw-up.”

Now we know that the New York Times was understating matters. A look-back investigation published over the weekend under the bylines of Apuzzo, Schmidt, Adam Goldman and Eric Lichtblau brings forth a stunning fact that frames the cataclysm over the New York Times’s exclusive: About two weeks before the paper’s scoop triggered such a backlash, the FBI had opened a criminal investigation into Clinton’s handling of classified information, under the code name “Midyear.” Here’s how the New York Times narrates the blowup:

On July 10, 2015, the F.B.I. opened a criminal investigation, code-named “Midyear,” into Mrs. Clinton’s handling of classified information. The Midyear team included two dozen investigators led by a senior analyst and by an experienced F.B.I. supervisor, Peter Strzok, a former Army officer who had worked on some of the most secretive investigations in recent years involving Russian and Chinese espionage.

There was controversy almost immediately.

Responding to questions from The Times, the Justice Department confirmed that it had received a criminal referral — the first step toward a criminal investigation — over Mrs. Clinton’s handling of classified information.

But the next morning, the department revised its statement.

“The department has received a referral related to the potential compromise of classified information,” the new statement read. “It is not a criminal referral.”

At the F.B.I., this was a distinction without a difference: Despite what officials said in public, agents had been alerted to mishandled classified information and in response, records show, had opened a full criminal investigation.

So: All of Washington in late July 2015 was debating how the New York Times had screwed up some references: criminal referral vs. security referral. The failure to nail that distinction, went the wisdom, exaggerated the story line in a way that harmed candidate Clinton. And the entire time, the FBI was in the launch stage of an actual, honest-to-goodness criminal investigation. The story, accordingly, understated the situation. “Had we known more, the story … wouldn’t have been better for the Clinton campaign,” says Apuzzo in a chat with the Erik Wemple Blog.

As it turned out, the FBI was way ahead of the New York Times. “It was sort of like, we were talking about the first step when they were on step five,” says Apuzzo. “We now know that I wasn’t the only one perplexed and confused about what had happened. This was an issue of tension at the FBI and they saw this weird parsing as giving cover to Hillary Clinton.” Indeed, Clinton herself referred to the proceeding as a “security review,” and not as a criminal investigation.

That it was, in fact, a criminal investigation became clear to the entire world in July 2016, when FBI Director James B. Comey publicly summarized the bureau’s findings. Though he slammed Clinton for careless use of a private email server for official business, he recommended that criminal charges were not “appropriate.” In a previous session with reporters, Comey balked at the way that Clinton was referring to the investigation. “We do investigations, not security inquiries,” he said.

There was a reason that the New York Times was a bit sluggish in appending corrections to the story, say both reporters: They were busy trying to square the information from their sources with the pushback coming from the Clinton campaign. “In hindsight, I wish that our sources had just said, ‘BS, the FBI opened up a criminal investigation two weeks ago,’ ” says Apuzzo. But they didn’t disgorge such precious information, and they were anonymous. “Because they just said, ‘You’re fine, you’re fine,’ we ended up writing an editor’s note.” In any case, those sources surely saw the links piling up on the Internet in condemnation of a pair of New York Times reporters. “If our sources were really, really good to us, they would have called us and said, ‘Hey, the criminal investigation is open,’ ” says Schmidt. “But we never got that call. I obviously wish that had happened.”

In a chat with the Erik Wemple Blog, Palmieri said that the New York Times’s allegations blindsided the Clinton campaign. “No one ever contacted our campaign to say we were under investigation,” says Palmieri. “All we knew is what the New York Times is telling us and then what the Justice Department is telling the New York Times.” Asked whether she now concedes that there was a criminal FBI investigation, Palmieri responds, “I’ll let the FBI continue to characterize whatever their investigation was or wasn’t.”

Goldman worked on the recent New York Times investigation but was on staff at The Post when the July 2015 Times story shook Washington. “I knew at the time there was a criminal investigation,” says Goldman, who is a friend of Apuzzo’s. “It’s the only kind of investigation they would have been doing. It was frustrating and it had a chilling effect on myself and, I’m sure, on other reporters about how we could accurately describe this story.” Time clarified matters, however. “Things started leaking out that allowed us to write what it was,” says Goldman, who in March 2016 reported in The Post that the Justice Department had granted immunity to a former State Department employee who’d worked on Clinton’s email setup. The story referenced “a criminal investigation into the possible mishandling of classified information.” Brian Fallon, a spokesman for the Clinton campaign, gave a statement for the piece: “As we have said since last summer, Secretary Clinton has been cooperating with the Department of Justice’s security inquiry, including offering in August to meet with them to assist their efforts if needed.”

When asked if he felt vindicated by the timeline, Apuzzo resisted yes. “I’m glad that it makes sense to me now. I just felt like it was intellectually important for me to understand” what went down. To the same question, Schmidt responds, “We took an enormous amount of criticism on it, and there’s no taking that back. Even if it turns out the punishment didn’t fit the crime, can’t change the punishment that we took at the time.” There was pain, too, for Apuzzo. “It was a really difficult time for me,” he says.

Neither reporter disputes that the original story misstated the sort of IG referral that washed up at the Justice Department. That vulnerability, says Schmidt, “allowed them to drive a Mack truck though the story.” “If there’s an error, it can be exploited and really used against you, so I learned a lot from it. It was an incredible learning experience,” he says.

Dean Baquet, the paper’s executive editor, was on the road and unavailable for an interview about all this stuff. As to whether the New York Times might revisit its editor’s note and corrections, Baquet said via email that it’s a “good question. It was, in fact, a criminal investigation. From the very beginning.”