– A crisis at the top of military leadership in the handling of a high-profile war crimes case has raised questions in the military community about the military justice system and what good order and discipline look like.

President Donald Trump’s interventions in several military justice cases, including that of Navy SEAL Eddie Gallagher’s, have military leaders debating whether the moves undermine the authority of military commanders.

Some Navy leaders said they are flummoxed by Trump’s interventions and their recent fallout, including the firing of Navy Secretary Richard Spencer. “He’s hammering away at the foundation of the military — good order and discipline,” said a senior Navy official. “The president essentially said he doesn’t trust one of his admirals’ judgment.”

Others say the breakdown occurred at the top rungs of military leadership, when Navy leaders tried to review Gallagher’s SEAL qualifications despite Trump’s wishes. “Good order and discipline starts at the top,” said Ed Hiner, a retired SEAL troop commander. “Someone gives you an order, you take it.”

On Nov. 15, Trump pardoned two soldiers — one convicted of murder — and granted clemency to Gallagher, reportedly over the recommendations of military advisers.

Gallagher was court-martialed this summer after several fellow SEALs accused him of committing war crimes during a 2017 deployment to Iraq. He was acquitted of most charges he faced but was convicted of one count of posing with an ISIS fighter’s corpse. For that, a military jury sentenced him to four months in the brig, which he served before his trial, and reduced him in rank one pay grade.

Trump released him from the brig before his trial; on Nov. 15 he restored his rank; and when news broke that the Navy planned a “trident review” board for Gallagher and four others, Trump tweeted that Gallagher was to retain his trident and remain a SEAL. The trident review board is an administrative process that usually takes place many rungs below the chain of command — far below the commander-in-chief level.