The Supreme Court on Friday evening decided, no, it was not going to needlessly insert itself in the military chain of command above President Joe Biden.

The Court’s decision in Austin v. U.S. Navy SEALs 1-26 largely halted a lower court order that permitted certain sailors to defy a direct order. A group of Navy special operations personnel sought an exemption from the Pentagon’s requirement that all active duty service members get vaccinated against Covid-19, claiming that they should receive a religious exemption.

A majority of the Court effectively ruled that, yes, in fact, troops do have to follow orders, including an order to take a vaccine.

The decision is undeniably a win for the balance of power between the executive branch and the judiciary that has prevailed for many decades. But the fact that the Court had to weigh in on this at all — not to mention that three justices, Justices Clarence Thomas, Samuel Alito, and Neil Gorsuch, dissented from the majority — is a worrisome sign about America’s judiciary.

As Justice Brett Kavanaugh explained in a brief opinion laying out why the lower court erred, this court “in effect inserted itself into the Navy’s chain of command, overriding military commanders’ professional military judgments.” Had the Court ruled the other way in SEALs, it would have effectively placed itself at the apex of the military’s chain of command, displacing Biden as commander-in-chief.

But as Kavanaugh correctly notes in his concurring opinion, there is a long line of Supreme Court precedents establishing that courts should be exceedingly reluctant to interfere with military affairs.

In Gilligan v. Morgan (1973), for example, the Court held that “the complex, subtle, and professional decisions as to the composition, training, equipping, and control of a military force are essentially professional military judgments,” and that “it is difficult to conceive of an area of governmental activity in which the courts have less competence.”

Nevertheless, Judge Reed O’Connor, a notoriously partisan judge in Texas who is best known for a failed effort to repeal the Affordable Care Act, ruled in favor of the service members who refused to follow a direct order. And the conservative United States Court of Appeals for the Fifth Circuit refused the Navy’s request to stay key parts of O’Connor’s order.

That left the responsibility of restoring the military’s proper chain of command to the Supreme Court. Though the Court’s order does not wipe out O’Connor’s decision in its entirety, it temporarily blocks that decision “insofar as it precludes the Navy from considering respondents’ vaccination status in making deployment, assignment, and other operational decisions.”

But the astonishing thing about the SEALs order is that the Supreme Court needed to intervene in this case at all.

Order prevailed, but several justices wanted to upend things

The most astonishing thing about the SEALs order is that at least three justices dissented. (While it is likely that six justices sided with the Navy here, only four justices — the three dissenters plus Kavanaugh — chose to reveal how they voted. So it is possible that one other justice silently dissented.)

Thomas did not explain why he dissented, but Alito published a brief opinion, joined by Gorsuch, which lays out why he thinks that judges should be allowed to countermand orders handed down to military personnel by their commanders. Among other things, Alito complains that the Navy did not provide service members with a meaningful process they could use to request a religious exemption from the vaccination requirement.

The Navy provided the Court with several statements from high-ranking officers explaining why it requires nearly every sailor to be vaccinated, and why it generally considers unvaccinated special warfare personnel undeployable.

According to Adm. William Lescher, the Navy’s second-highest-ranking officer, Navy vessels have only limited medical facilities. So, if one of the ship’s crew becomes seriously ill, that “would require a return to port or an emergency medical evacuation by helicopter” — potentially forcing the whole ship to abandon its mission to accommodate one unvaccinated service member.

Special warfare personnel, moreover, often deploy in very small units. So one member becoming sick is a big blow to the team. And, the Navy argued, special operations “are often conducted in hostile, austere or diplomatically sensitive environments” where a severely ill service member might not be able to obtain local medical care and may need to be evacuated by the Navy — an operation that is itself dangerous and that could force the sick service member’s fellow sailors to risk their lives on his or her behalf.

To these concerns, Alito essentially said, “Prove it.”

“In order to win at trial,” Alito wrote in response to the Navy’s warnings, “it would not be enough for the Government to posit that sending an unvaccinated Seal on such a mission might produce such consequences.” Rather, the Navy would have to prove that requiring vaccination “is the least restrictive means of furthering the interest it asserts in light of the present nature of the pandemic, what is known about the spread of the virus and the effectiveness of the vaccines, prevalent practices, and the physical characteristics of Navy Seals and others in the Special Warfare community.”

I want to emphasize the sheer enormity of what Alito is suggesting here. Once the Supreme Court permits a single servicemember to defy a direct order, that opens the door to any member of the armed services who disagrees with an order running to court to seek an exemption.

Think of the kinds of orders that military personnel have to obey — “take that hill,” “guard this prisoner,” “cease fire.” And even if Alito did not intend for his dissent to apply to such battlefield orders, his dissent could effectively neutralize major military assets while religious liberty cases brought by service members are being litigated. Imagine, for example, if the captain of an aircraft carrier is ordered to deploy his ship close to Ukraine — but the captain refuses because, for religious reasons, that captain believes that Vladimir Putin should prevail in his war against Ukraine.

The Court has understood for many decades that the military simply cannot function if its members think orders may be optional. As the Supreme Court held in Goldman v. Weinberger (1986), “the essence of military service ‘is the subordination of the desires and interests of the individual to the needs of the service.’”

Permitting service members to seek exemptions from the courts, Goldman explains, would undermine service members’ “habit of immediate compliance with military procedures and orders” — a habit that “must be virtually reflex with no time for debate or reflection.”

At the end of the day, every service member must know who their commander is, and everyone must respect the chain of command. There can only be one person at the apex of that chain, and it can either be Joe Biden or Samuel Alito.

And, as Kavanaugh notes in his opinion, the Constitution is very clear about who is at the top of that chain. It says, in unambiguous terms, that “the President shall be commander in chief of the Army and Navy of the United States.”