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Losing the story to another news outlet would have been a far, far better outcome than publishing an unfair story and damaging the Times’s reputation for accuracy.

New York Times public editor Margaret Sullivan on July 27, 2015

Late on July 23, 2015, the Times delivered another bombshell. A front-page article headlined “Criminal Inquiry Is Sought in Clinton Email Use” reported that two Inspector Generals had asked the DOJ “to open a criminal investigation into whether sensitive government information was mishandled in connection with the personal email account Hillary Rodham Clinton used as Secretary of State.” Now my campaign had to deal with questions about whether I was being measured for an orange jumpsuit.

The Justice Department, however, clarified quickly that it had “received a referral related to the potential compromise of classified information” but “not a criminal referral.” The Times had to publish two corrections and an editor’s note explaining why it had “left readers with a confused picture.”

Representative Elijah Cummings, the ranking Democrat on the Benghazi Committee, helped explain what happened: “I spoke personally to the State Department Inspector General on Thursday, and he said he never asked the Justice Department to launch a criminal investigation of Secretary Clinton’s email usage. Instead, he told me the Intelligence Community IG [Inspector General] notified the Justice Department and Congress that they identified classified information in a few emails that were part of the FOIA review, and that none of those emails had been previously marked as classified.”

Looking back after the election, the Times described the mix-up as “a distinction without a difference,” because we now know that there was an investigation under way. But we also now know that there was a disagreement between the Department of Justice and the FBI about how to describe it appropriately. The DOJ’s approach, reflected in the clarification to the Times story issued by its spokesperson, was intended to adhere to the long-standing policy of not confirming or denying the existence of an investigation—a rule that Comey respected scrupulously when he refused to say anything at all about the investigation into possible ties between Russia and the Trump campaign. But when it came to my emails, he had plenty to say. Regardless, the Times got into trouble because it gave its readers only one side of the story. The paper’s Margaret Sullivan published a scathing postmortem headlined, “A Clinton Story Fraught with Inaccuracies: How It Happened and What Next?” Sullivan took the Times to task for its shoddy reporting. “You can’t put stories like this back in the bottle—they ripple through the entire news system,” she wrote. “It was, to put it mildly, a mess.”

If all these respected, senior foreign service officers and experienced ambassadors are sending these emails, then this issue is not about how Hillary Clinton managed her email, but how the State Department communicates in the 21st century.

—Phil Gordon, a former Assistant Secretary of State and National Security Council official, who had some of his emails to me classified retroactively, in the Times, May 10, 2016

The Department of Justice’s investigation, and pretty much everything else that followed, turned on questions of classification. The issue was no longer using personal email on the job. The question now was what should be considered classified, and did I or anyone else intend to mishandle it?

Despite its science-y name, classification isn’t a science. Five people asked to look at the same set of documents could easily come to five different decisions. We see this every day across the government as different agencies disagree about what information should be considered classified. When I was Secretary, it was not uncommon for one of our Foreign Service Officers talking to foreign diplomats and journalists to report back on political or military developments in a country and file this information in an unclassified form. But a CIA agent in the same country, using covert informants and techniques, might gather the very same facts yet classify the report as secret. The very same information: Is it classified or not? Experts and agencies frequently disagree.

That’s what happened when the State Department and the intelligence agencies reviewed my emails for release. Remember, I had asked for all of them to be published so that the American people could read them and judge for themselves. There were also a number of Freedom of Information Act requests working their way through the courts. The easiest thing to do would have been to just dump every email onto a website and be done with it, but the government has rules it has to follow in FOIA cases. You don’t want to accidentally publish someone’s Social Security number or cell phone number.

When reviewing my thirty thousand emails, in a number of instances, representatives of various U.S. intelligence agencies sought to retroactively classify messages that had not previously been marked as classified. Many State Department diplomats with long experience conducting sensitive diplomacy disagreed with those decisions. It was like a town changing speed limits and retroactively fining drivers who had complied with the old limit but not the new one.

For example, an email from Dennis Ross, one of our country’s most experienced diplomats, was declared classified retroactively. It described back-channel negotiations he’d conducted with Israelis and Palestinians as a private citizen back in 2011. Government officials had already cleared him to publish the same information in a book, which he had done, but now different officials were trying to classify it. “It shows the arbitrariness of what is now being classified,” Dennis observed.

Something similar happened to Henry Kissinger around the same time. The State Department released the transcript of a 1974 conversation about Cyprus between then-Secretary of State Kissinger and the director of the CIA, but much of the text was blacked out because it was now considered classified. This puzzled historians because State had published the full, unredacted transcript eight years before in an official history book… and on the department’s website!

Another veteran diplomat, Ambassador Princeton Lyman, was also surprised to find some of his run-of-the-mill emails to me retroactively designated as classified. “The day-to-day kind of reporting I did about what happened in negotiations did not include information I considered classified,” he told the Washington Post.

That is an absurdity. We might as well shut the department down.

—Former Secretary of State Colin Powell in the Times on February 4, 2016, after learning that two messages sent to his personal email account were being classified retroactively

Like Colin, I thought it was ridiculous that some in the intelligence agencies were now trying to second-guess the judgment of veteran diplomats and national security professionals in the State Department about whether messages they sent should be classified. It was doubly ridiculous to suggest that I should have second-guessed them in the moment.