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WASHINGTON — In an extraordinary move, Pentagon confirmed today that the Navy secretary has been fired for going outside his chain of command by proposing a “secret agreement with the White House,” according to a senior defense official.

The agreement that led to Navy Secretary Richard Spencer’s forced resignation involved the case of Navy SEAL Eddie Gallagher, one of three service members facing war crimes allegations whose cases have caused unprecedented tension between the Pentagon and President Donald Trump.

Spencer had appeared to be seeking a way to resolve a standoff between the Pentagon and White House over Gallagher’s case, but competing narratives that emerged in the chaotic hours after Spencer’s dismissal suggest the depth of the upheaval, disconnection, and discord that remains.

Trump suggested on Twitter that Spencer’s dismissal had to do with cost overruns and the way Gallagher had been treated by the Navy. Defense Secretary Mark Esper said he asked Spencer to resign because he had lost “trust and confidence in him regarding his lack of candor,” according to a Pentagon spokesman.

And Spencer pointed squarely to the President, suggesting that Trump was undermining the “key principle of good order and discipline” of the US military by intervening in Gallagher’s case.

“I cannot in good conscience obey an order that I believe violates the sacred oath I took in the presence of my family, my flag and my faith to support and defend the Constitution of the United States,” Spencer wrote in his letter to the President acknowledging his termination.

Gallagher had been convicted of bringing discredit to the armed services after posing next to a dead ISIS fighter’s body, which is against regulations. He was demoted for that offense and acquitted of a separate murder charge. After Trump reversed Gallagher’s demotion a week ago, military officials launched a formal review to determine if Gallagher was fit to serve, which is protocol after a conviction. That review was expected to lead to his expulsion.

Gallagher issued a statement on Sunday evening thanking his family, legal team and supporters that ended by heaping praise on Trump.

“President Donald Trump you have my deepest gratitude and thanks. You stepped in numerous times and showed true moral fiber by correcting all the wrongs that were being done to me. You are a true leader and exactly what the military and this nation needs,” Gallagher said.

(PHOTO: Alex Brandon/AP/CNN)