The email in question was forwarded to Clinton in November 2012 and referred to the possible arrests of suspects in the September 11 Benghazi terrorist attacks. The State Department ultimately released a redacted portion of it in May 2015 along with thousands of other Clinton emails.

To Republicans and the Donald Trump campaign, this disclosure is a smoking gun—evidence that the State Department, working on Clinton’s behalf, fought the FBI’s desire to classify emails after the fact in order to downplay security concerns associated with her private server.

“These FBI documents provide undeniable proof that Hillary Clinton colluded with the FBI, [the Department of Justice] and State Department to cover up criminal activity at the highest levels,” General Michael Flynn said in a statement for the Trump campaign. The Republican National Committee added: “The Obama Administration's blatant attempts to shield Hillary Clinton from accountability for her reckless conduct will only inflame the growing distrust Americans have for their own government.”

Even Republicans who have been warring with Trump lately chimed in. House Speaker Paul Ryan said the disclosure “bears all the signs of a cover-up,” while the chairmen of the House oversight and intelligence committees called for President Obama and Secretary of State John Kerry to remove Kennedy from his post pending a full investigation.

The State Department rushed to Kennedy’s defense. The department’s chief spokesman, Mark Toner, all but accused the FBI official of lying about his conversation with Kennedy.

“The allegation of any kind of quid pro quo is inaccurate and does not align with the facts,” Toner told reporters at a press briefing. “There was no quid pro quo.”

He acknowledged that Kennedy challenged the FBI on its decision to mark the 2012 email classified, as government officials do routinely in disputes over what should be secret and what should not be. But Toner said it was the FBI official—not Kennedy—who brought up the possibility of allowing more agents to be stationed in Baghdad and that he did so after the conversation about the email, not at the same time. Basically, Toner said, the FBI official “took advantage” of the fact that he had Kennedy on the phone to bring up an unrelated matter.

Why, then, did the FBI official accuse Kennedy of explicitly proposing a quid pro quo. “I can’t speak to what his or her intentions were,” Toner said. The official, he added, was “clearly expressing a personal opinion about what happened.”

The documents the FBI released on Monday were summaries of the interviews it conducted in its investigation of Clinton, not entire transcripts. And the bureau released its own statement backing up the State Department’s claim that it was the FBI official, who is now retired, who brought up the separate matter of the overseas deployments.

Prior to the initiation of the FBI’s investigation of former Secretary Clinton’s personal email server, the FBI was asked to review and make classification determinations on FBI emails and information which were being produced by the State Department pursuant to FOIA. The FBI determined that one such email was classified at the Secret level. A senior State Department official requested the FBI re-review that email to determine whether it was in fact classified or whether it might be protected from release under a different FOIA exemption. A now-retired FBI official, who was not part of the subsequent Clinton investigation, told the State Department official that they would look into the matter. Having been previously unsuccessful in attempts to speak with the senior State official, during the same conversation, the FBI official asked the State Department official if they would address a pending, unaddressed FBI request for space for additional FBI employees assigned abroad. Following the call, the FBI official consulted with a senior FBI executive responsible for determining the classification of the material and determined the email was in fact appropriately classified at the Secret level. The FBI official subsequently told the senior State official that the email was appropriately classified at the Secret level and that the FBI would not change the classification of the email. The classification of the email was not changed, and it remains classified today. Although there was never a quid pro quo, these allegations were nonetheless referred to the appropriate officials for review.​

The FBI did not say what the outcome of that review was, nor did it identify the official who made the allegations against Kennedy. Congressional Democrats noted that the State Department’s inspector general investigated whether there was “undue or inappropriate influence” exerted during discussions over the classification and release of Clinton’s email. In a report to the House oversight committee in January, the inspector general found that there was not.