This image provided by the Office of the Director of National Intelligence shows deputy national intelligence director Sue Gordon. President Donald Trump says Gordon has announced she is leaving her position. (Office of the Director of National Intelligence via AP)
Office of the Director of National Intelligence/AP
This image provided by the Office of the Director of National Intelligence shows deputy national intelligence director Sue Gordon. President Donald Trump says Gordon has announced she is leaving her position. (Office of the Director of National Intelligence via AP)
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(CNN) —  

The country’s No. 2 intelligence official, Sue Gordon, knew it was likely she would have to eventually step down from her post, but the timing of that decision became more urgent on Thursday after her boss – outgoing spy chief Dan Coats – interrupted a meeting she was holding on election security and asked his deputy to submit her letter of resignation, sources familiar with the events told CNN.

While details of the conversation between Gordon, an intelligence veteran of more than 30 years, and Coats remain unclear, sources say that the situation clearly abruptly changed after the meeting was interrupted.

Shortly after her encounter with Coats, Gordon submitted her letter of resignation to Vice President Mike Pence, though the document itself was addressed to Trump, according to officials, a highly unusual move that prompted some confusion among some West Wing officials who waited for the President’s tweet confirming the news.

Not surprised

Ultimately, White House officials told CNN they were not surprised by the fact that Gordon chose to resign, as it was clear the President was never going to select her for the top job, or even the acting position.

White House officials had been signaling such a move for days, saying the President would prefer to have a political loyalist in the acting role until a permanent nominee is selected.

While Trump has said in recent days that he liked Gordon personally, officials said that he believed she was too closely tied to individuals in the intelligence world, such as former CIA Director John Brennan and even Coats himself, a theory some advisers pushed.

Under normal protocol, Gordon would have become acting director after Coats resigned. But administration officials told CNN that the White House was reviewing whether it could legally choose an acting director outside the line of succession.

The circumstances surrounding Gordon’s resignation, including the role Coats appears to have played in the timing of her announcement, seem to indicate she was forced out for political reasons.

“I offer this letter as an act of respect & patriotism, not preference. You should have your team,” she wrote in a handwritten note to the President that was released by the White House.

Gordon’s abrupt departure, with only one week’s notice, and Trump’s longstanding hostility toward the intelligence community – which he has publicly derided, likened to Nazis and disagreed with – is likely to heighten concerns that the President may be trying to politicize agencies that are meant to stand apart from partisanship or politicking.

Intelligence professionals emphasize the need to keep politics out of their work in order to offer policy makers the clearest assessment they can of threats and opportunities.

Yet, Trump has made clear his desire to bring to heel US intelligence agencies, which have produced evidence he disagrees with on Iran, North Korea, Russia’s interference in US elections and other issues.

When discussing his attempt to replace Coats with Texas Republican Rep. John Ratcliffe on July 30, the President told reporters that intelligence community needed “somebody like that that’s strong and can really rein it in. As you’ve all learned, the intelligence agencies have run amok. They’ve run amok.”

But the dramatic implosion of Ratcliffe’s nomination last week only fueled uncertainty surrounding who would be tapped to lead the intelligence community, both in an acting capacity and as the permanent choice.

Leaders in both parties had expressed confidence in Gordon, with many advocating for her to get the top job. Her departure is likely to unsettle lawmakers eager for stability in the aftermath of Coats’ resignation and the fallout after Trump’s chosen successor, Ratcliffe, fell by the wayside after scathing criticism.

“Sue Gordon’s retirement is a significant loss for our Intelligence Community,” said Sen. Richard Burr, the North Carolina Republican who chairs the Senate Intelligence Committee.

Trump addressed one of those questions Thursday after Gordon’s resignation, naming Joseph Maguire, the leader of the National Counterterrorism Center, as his interim choice.

’A great job’

Maguire “has a long and distinguished career in the military, retiring from the US Navy in 2010. He commanded at every level, including the Naval Special Warfare Command. He has also served as a national security fellow at Harvard University.

“I have no doubt he will do a great job!” the President tweeted.

Current and former intelligence officials have acknowledged that they are unhappy with the way Gordon is having to retire and noted that her departure is a blow to the community due to her level of experience and track record of speaking the truth.

But at the same time, Trump’s decision to name Maguire as acting DNI is not expected to prompt any sort of mass exodus or overwhelming outrage from career intelligence professionals, one official told CNN.

This official added that Maguire is well respected within the intelligence community, particularly due to his military background and is not viewed as an overly partisan pick for the acting DNI position.

“Maguire’s deep military background and work at NCTC means that he brings to the job a welcome understanding of IC capabilities and experience with current policy and IC leadership. However, his assignment to the acting position means that NCTC is deprived of his leadership at a time when the policy community is grappling with the issue of domestic terrorism,” a former senior intelligence official said.

“I am confident, however, that this leadership shuffle will have little impact on ongoing IC operations,” the former official said.

Vice Chairman of the Senate Intelligence Committee Mark Warner said Friday that he expects Maguire to embody the same apolitical leadership style as both Coats and Gordon.

“Given the circumstances of his appointment as Acting DNI, it is more important than ever that Admiral Maguire stands by that commitment to speak truth to power,” Warner said in a statement. “His success or failure in this position will be judged by the quality of work produced by the intelligence community, not by how those intelligence products make the President feel.”

CNN’s Kaitlan Collins, Alex Marquardt and Nicole Gaouette contributed reporting.