When a team of Navy SEALs slipped undetected into Pakistan in the predawn hours of May 1, 2011 and returned with Osama bin Laden’s the corpse, the world was exposed to the ability and reach of America’s elite commando units. In the years that followed, as SEALs took an oversized share of the burden in fighting against terrorists in far-flung corners of the globe, their heroic exploits were documented — and often dramatized — in an uninterrupted production line of books, movies and television shows.

Yet over the last two years, it’s often been SEALs’ behavioral misconduct that has captured national headlines, including accusations of war crimes; involvement in the alleged murder of a Green Beret in Africa; allegations of sexual assault and drinking on the job; snorting cocaine and cheating urinalysis screening; and the sexual abuse of a five-year-old child.

President Donald Trump’s meddling into the case of Chief Petty Officer Edward Gallagher, a Navy SEAL who was accused by his teammates of fatally stabbing an unarmed, captured ISIS fighter and attempting to murder Iraqi civilians during a 2017 deployment, incensed current and former military leaders who say the interference is without precedent in American history. In the long term, they say, it could destabilize attempts to address the long-standing problems plaguing one of the nation’s front-line defenses against transnational threats.

Michael Lumpkin, a retired Navy SEAL commander and former Assistant Secretary of Defense for Special Operations and Low-Intensity Conflict, said it’s within the President’s authority to inject himself into individual legal cases under military jurisdiction prior to adjudication. “But was it the right thing to do? No,” he says. “It shows undue political influence on military justice and administrative processes as well as undermines current efforts that have been undertaken to reform the force.”

This summer, a military jury acquitted Gallagher of the murder charges but convicted him of posing in a photo with the fighter’s corpse. The court-martial jury sentenced him to four months confinement, time which had already been served, but also called for a reduction in rank — a move that would slash his pay by two-thirds just weeks before the 19-year-veteran intended to retire.

Enter Trump, who has taken on Gallagher’s case in a personal endeavor he says will “protect our great warfighters.” On Nov. 11, Trump restored Gallagher’s rank and on Monday he stripped the Navy of its attempt to move forward with a review process that would determine whether or not Gallagher should remain in the SEALs. The decision to halt that assessment, which would have been conducted by a panel of SEALs, was a rebuke to Naval Special Warfare commander Rear Adm. Collin Green who had just days earlier launched the review process determine whether Gallagher deserved to belong within the SEAL community.

The Navy has expelled 154 sailors from the SEALs since 2011, stripping them of the right to wear the gold Trident pins that signify membership. None of those cases have achieved national attention like the Gallagher case. “How can Admiral Green be asked to clean up the bad behavior in the SEAL community if you take away his only way to hold people accountable?” says Stuart Bradin, a retired Green Beret colonel and president of the Global SOF Foundation, a non-profit association for Special Operations forces. “The SEALs should be allowed to decide who can remain a SEAL. Anything less sends the wrong signal to everyone who’s doing their job the right way. You need to make examples of people.”

U.S. officials close to Green say he never planned to make an example of Gallagher. He just wanted to hold Gallagher to the same standard that all SEALs are held to when Trump waded into the case. Defense Secretary Mark Esper, Joint Chiefs of Staff Gen. Mark Milley and former Navy Secretary Richard Spencer agreed with Green that even though Gallagher exonerated from murder allegations, he should still face a review board to decide whether he could retire as a SEAL. But Trump ignored their advice. Spencer resigned over the ordeal on Nov. 24. “I cannot in good conscience obey an order that I believe violates the sacred oath I took,” he wrote in his resignation letter.

Spencer’s departure raises questions about Green’s future atop the SEALs, as well as the Trump Administration’s appetite for ethical reform inside the Special Operations community. If Green does survive, he must continue on his effort to clean up the SEALs image without weighing in on one of the highest profile military justice cases in the post-9/11 era. “Can he still be effective?” asks David Cooper, a retired command master chief of SEAL Team Six. “This could be an opportunity for him. Visit the troops, take the rank off, so to speak, and just listen. Really invite people in the community to talk and share their concerns without judgment or rationale, to empathize. And to ask the questions: Who are we? Who do we want to be? What’s happening and how should we go forward?”

But there are fears that a chilling effect on speaking out on bad actors within the SEALs may take place among the ranks as a result of the Gallagher case. Several SEALs testified against him — an extremely rare occurrence in such cases — and are expected to be ostracized from the community as a result. Cooper dismissed the idea that the high-profile case will prevent people from talking. “The vast majority of soldiers, sailors, airmen, and marines are bound by ethical behavior that emanates from within the service members,” he says. “Most people don’t cotton to such behavior, and the few that do will continue to be held accountable. I hope my optimism isn’t naivete — I don’t believe it is. But only time will tell.“

What has happened, Cooper says, is the emergence of a so-called “Gallagher Effect,” in which leadership overreacts to relatively minor problems at the highest tiers of Naval Special Warfare Command. In July, Green made a command-wide order that SEALs follow strict grooming and uniform standards that is required by conventional sailors. It was a major break from tradition for SEALs, who like other U.S. special operators, are allowed to grow out their hair and beards in war zones. Commanders were also ordered to routinely inspect SEALs appearances and facilities to ensure standards were met. “We must take a ‘back to basics’ leadership approach to correct our drift,” Green, who has launched a broader review of the ethics and culture within the SEAL community, wrote in a memorandum.

Commander Tamara Lawrence, a Naval Special Warfare Command spokeswoman, would not comment on how the Gallagher case has affected Green’s reform efforts, but did issue a statement: “[Rear Admiral] Green is focused on his job as the commander of Naval Special Warfare, delivering a capable, ready, and lethal maritime special operations force in support of national security objectives,” she said.

It is becoming increasingly clear that endless wars abroad result in more than financial costs. Ceaseless deployment cycles among Special Operations forces have caused problems at home, driving the Pentagon to create a task force to address drug and alcohol abuse, family crises and suicide among the ranks. U.S. Special Operations Command, which oversees all of the country’s most elite forces, including Navy SEALs, Army Green Berets, Marine Corps Raiders and others, reported suicides tripled to 22 deaths in 2018.

The high-operations tempo also raises the chances of battlefield mistakes — or worse, war crimes on the battlefield. The stress, both physical and psychological, has strained the SEALs, and more broadly, the U.S. Special Operations community. In August, the command launched its own ethics review.

The inquiry has yet to be completed, but when it is, it will be the second time in as many years that the command is studying whether an institutional rot resides within its ranks. “The American people must trust those who protect them, including the special operations professionals in this command,” Gen. Richard Clarke, Special Operations commander, wrote in a memo about the review. “This is about making us better.”

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Write to W.J. Hennigan at william.hennigan@time.com.