The Navy SEAL at the center of one of the highest-profile war crimes cases in years had his sentence drastically reduced Tuesday by the Navy’s top admiral, sparing the SEAL from the most serious punishment he still faced, a steep demotion that would have cost him hundreds of thousands of dollars in retirement pay.

The unusual act of clemency comes in the case of Chief Petty Officer Edward Gallagher, who a year ago was facing a court-martial and the prospect of life in prison without parole. Navy prosecutors had accused him of shooting civilians in Iraq, killing a captive enemy fighter with a hunting knife, and threatening to kill fellow SEALs if they reported him, among other charges. Gallagher was acquitted by a military jury in July of all the charges except one minor count: Bringing discredit on the armed forces, by posing for a photo with the corpse of the captive he was accused of killing.

Adm. Mike Gilday, the Chief of Naval Operations, did not erase the conviction or relieve Gallagher of all punishment, as the defense had asked. Instead, he limited the sentence to a demotion by one rank, to special operator first class, as the jury had recommended. The Navy said in a statement that the admiral “thoroughly reviewed the record of trial, along with the clemency request submitted by the defense,” before issuing the decision.

The case was closely watched by President Donald Trump, who intervened several times on the special operator’s behalf and congratulated him on Twitter when he was acquitted of nearly all charges, saying, “Glad I could help!”

Gallagher’s lawyers said they were disappointed that the Navy let the demotion stand, and said they will seek to have it reversed, though they declined to say how.

“We beat all the serious charges at trial, despite the fact that Eddie’s case was contaminated by government misconduct from the get-go” said one of his lawyers, Marc Mukasey, who also represents Trump in some personal matters. “The photo charge should never even have reached a courtroom,” Mukasey said. “Stay tuned. This fight isn’t over.”

Timothy Parlatore, another lawyer for Gallagher, said that his client wanted to retire as a chief, and that he would continue to push to have his rank restored, though not by appealing directly to Trump.

“If the president hears about this and decides to do something on his own, that’s something else, and he can do that,” Parlatore said.

Navy leaders initially intended to punish Gallagher more harshly, including administrative sanctions as well as his sentence, Navy officials said. But the leaders came to believe that any adverse action would be reversed by Trump, perhaps derailing the careers of Naval officers in the process. After the court-martial verdict, Trump angrily ordered the Navy to strip commendations from the prosecutors in the case.

In recent weeks, Gallagher has appeared defiant in social media posts, including one where he called top Navy leaders “a bunch of morons.” Another recent post announced that he planned to leave the Navy and start a clothing line.

On Tuesday he posted a photo on Instagram showing him with the president’s embattled personal lawyer, Rudy Giuliani, with the comment, “Had the honor to meet Rudy Giuliani in New York last night — Great man & thank you for all you do for our country.” Mukasey and Giuliani were formerly law partners.

Gallagher was acquitted of the most serious charges, but his lone conviction still threatened to carry a heavy price when the jury sentenced him to 120 days’ confinement. Though he would not actually have to serve any of that time, because he had already been confined for longer — more than 200 days — as he awaited trial, such a sentence carries with it an automatic reduction in rank to seaman recruit, the lowest in the Navy. His lawyers said that retiring from the Navy at that rank could have cost him nearly $1 million in retirement pay, compared with what he would have expected to receive after retiring as a chief.

Under military law, the top officer overseeing the court-martial, known as the convening authority, can reduce a sentence imposed by a jury or overturn a conviction altogether in certain circumstances.

Gallagher’s lawyers argued in letters to Navy leaders that the SEAL, a decorated veteran of multiple combat tours, deserved clemency because he had been held in confinement for so long before trial, had been denied a promotion and a Silver Star medal, and had seen his children taken out of their house by armed Navy investigators during a search.

They also argued that taking trophy photos with dead bodies is a relatively common practice in the military that, while illegal, is rarely prosecuted, and that the Navy had targeted the SEAL unfairly.

“Chief Gallagher faces a draconian punishment that does not fit the conduct,” Parlatore wrote in a request for clemency. “It will inflict unnecessary and irreparable harm on his wife, children, and the equity of the military justice system.”

The pleas for leniency were initially rebuffed over the summer by the convening authority in the case, Rear Adm. Bette Bolivar, the commander of Navy Region Southwest. In a letter to Parlatore, Bolivar said that she found Gallagher’s behavior after his trial reprehensible, and that she had no intention of reducing his sentence.

Trump then called the Chief of Naval Operations at the time, Adm. John M. Richardson, to a White House meeting where Gallagher’s case was discussed. Richardson took authority over the case from Bolivar a few days later; it passed to Gilday when Richardson retired in August.

Gilday’s decision to reduce Gallagher by only one rank will still cost the SEAL nearly $200,000 in retirement pay, according to his lawyers’ estimate. And the SEAL could still face administrative punishment for other misconduct that the Navy investigated but did not include in the court-martial.

Military lawyers say that clemency is nearly always requested after a court-martial conviction, but it is rarely granted, and that having the top admiral in the Navy take over authority for a case is nearly unheard-of.

“In my 15 years of military law, I’ve never seen it,” said Patrick Korody, a former Navy prosecutor who has followed the Gallagher case. “But there is a feeling among military lawyers that the defense has just steamrolled everyone below, so giving it to the CNO is the right decision. He has authority to do the proper thing.”

Despite the grim details of the case, Korody said, clemency for the SEAL, who led a platoon in combat in Iraq, was not unreasonable.

“Maybe as a leader, Gallagher should have known better — we don’t want our service members taking pictures of corpses as if they are trophies,” Korody said. “But is that something we take someone’s retirement for? The convening authority should take into account his long record of service, and whether he has mental health issues from his deployments.”

The case has been unusual from the start. Gallagher was reported to authorities by his own men, who told investigators that they initially admired their platoon leader when they were deployed to Iraq in 2017 to help clear Islamic State fighters from the city of Mosul. But once on the ground, they said, he became fixated on killing. When a wounded Islamic State fighter was brought in, three SEALs told investigators, they saw their chief stab the fighter in the neck, killing him. Others in the platoon said they saw him shoot down a girl and an old man with a sniper rifle.

As the trial neared, the Navy prosecutors’ case began to fall apart. Most of the platoon refused to speak to investigators. The Gallagher family took to conservative TV and radio, accusing platoon members who did come forward of lying. The lead prosecutor was removed after emails with tracking software was sent to defense lawyers in an effort to trace leaks. And a star witness changed his story on the stand.

A jury made up almost entirely of ground troops with combat experience deliberated for a little more than eight hours before finding the chief not guilty of all but the single count involving the trophy photo.

The lightened punishment for Gallagher could have broad repercussions for the Navy SEAL teams, which have been openly grappling with what the SEALs’ leader, Rear Adm. Collin Green, has called an “ethics problem.”

The SEALs who came forward about Gallagher’s actions said Gilday’s decision was a disappointment. Two of them left the Navy as a result of their experiences on the deployment and during the court-martial. Others, fearful that Gallagher’s many supporters would undermine their careers, are also thinking about leaving the military.

“These guys tried to do the right thing,” said one active-duty SEAL who asked that his name not be used because he feared retribution. “And when they did, they saw that some of their good friends wouldn’t stand up for them. I think they realized the so-called brotherhood wasn’t what they thought it would be.”