Updated at 6:25 p.m. ET
President Trump told reporters at the White House that he was "sticking up for the armed forces" in his pardons of military personnel.
The commander in chief has repeatedly intervened on behalf of the Navy SEAL recently convicted of misconduct. And Defense Secretary Mark Esper said Trump did it again over the weekend, directly ordering him to allow Chief Petty Officer Eddie Gallagher to retire as a SEAL.
"I spoke with the president on Sunday. He gave me the order that Eddie Gallagher will retain his Trident pin," Esper told reporters on Monday at the Defense Department, referring to the insignia designating Gallagher as a member of the elite commando force.
The order from the commander in chief effectively put an end to proceedings by a Trident review board that were called by the commander of Navy special warfare, Rear Adm. Collin Green. The panel was charged with deciding whether Gallagher and three of his supervising officers were fit for duty. In Gallagher's case, the board was set to convene next week.
On Monday, Esper also reiterated his reasons for asking Navy Secretary Richard Spencer to tender his resignation on Sunday. He accused Spencer of circumventing the appropriate channels, including Esper himself, to engage in direct negotiations with the White House to allow Gallagher to remain a SEAL. Meanwhile, Spencer was saying publicly that the Trident review board process should be allowed to play out.
"This proposal was completely contrary to what we agreed to and contrary to Secretary Spencer's public position," Esper said, adding that he was "completely caught off guard by this information and realized that it had undermined everything we had been discussing with the president."
Esper tried to undo the perception that Spencer's dismissal was tied to the specifics of Gallagher's case, saying instead that it was over the chain of command.
Hours later Trump pushed back for granting clemency to Gallagher and pardoning two Army officers earlier this month.
He said it was an unfair to try put away "warriors" like Gallagher, Army Captain Clint Lorance and Maj. Matthew Golsteyn. Lorance was convicted of murder six years ago while Golsteyn was about to face trial for the alleged murder of a Taliban bombmaker.
"We're not going to do that to our people," Trump said.
The move went against the advice of military leaders.
He also criticized former President Barack Obama for commuting the sentence of Chelsea Manning, a soldier who was convicted of leaking classified documents.
The standoff between Trump and the Navy's top brass began even before Gallagher's court-martial trial over the summer. Gallagher, who served multiple tours in Iraq, was accused of a slew of crimes, including the murder of a wounded Islamic State prisoner. In the end, he was acquitted of all but one charge — posing with a dead detainee. Part of his sentence included a demotion to the lower rank of petty officer first class.
Trump subsequently overturned that decision, commanding the Navy to promote Gallagher back to chief petty officer.
Green's decision to initiate a review of Gallagher's fitness as a SEAL was seen as a rebuke of the president's order.
In his resignation letter, Spencer suggested that his dismissal was indeed connected to Gallagher's review rather than any communication back channels.
"Unfortunately it has become apparent that in this respect, I no longer share the same understanding with the Commander in Chief who appointed me, in regards to the key principle of good order and discipline," Spencer wrote. "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."
On Sunday, Trump also linked Spencer's ouster to Gallagher. "I was not pleased with the way that Navy Seal Eddie Gallagher's trial was handled by the Navy. He was treated very badly but, despite this, was completely exonerated on all major charges. I then restored Eddie's rank," the president tweeted.
Then he introduced another reason for pushing Spencer out: "Large cost overruns from past administration's ... contracting procedures were not addressed to my satisfaction."
The president added that he would nominate Kenneth Braithwaite as the next Navy secretary. "A man of great achievement and success, I know Ken will do an outstanding job!" Trump said.
Gallagher's attorney, Timothy Parlatore, told the Navy Times that neither he nor his client foresaw such fallout. "With this personnel change, this institution will improve and no one will go through the ordeal Eddie went through. At the end of the day, the most important duty any of us have is protecting America," Parlatore said.
"This case is completely bananas," he added.
Gallagher said he is "overjoyed" that the president stepped in on his behalf once again. In an interview on Fox & Friends that aired Sunday morning, Gallagher name-checked Green and Spencer.
"This is all about ego and retaliation. This has nothing to do with good order and discipline. They could have taken my Trident at any time they wanted. Now they're trying to take it after the president restored my rank," Gallagher said.
It is unclear where the events of the last few days leave the Trident review board proceedings for Gallagher's three supervising officers: Lt. Jacob Portier, Lt. Cmdr. Robert Breisch and Lt. Thomas MacNeil.
A previous version of this story said then-President Obama had pardoned Chelsea Manning, who was convicted of leaking classified documents. Obama commuted Manning's sentence.