An ongoing legal battle over whether the military can force troops to get vaccinated against COVID-19 has left the Navy with a warship they say they can’t deploy because it is commanded by an officer they cannot fire.

It’s a standoff the brass are calling a “manifest national security concern,” according to recent federal court filings.

The issues stem from a lawsuit filed in the U.S. District Court for the Middle District of Florida late last year alleging servicemembers’ rights are being infringed upon by the COVID vaccine mandate because their religious beliefs prevent them from taking the vaccine.

Judge Steven D. Merryday issue an order last month banning the Navy and Marine Corps from taking any disciplinary action against the unnamed Navy warship commander and a Marine Corps lieutenant colonel for refusing the vaccine.

In the process, the case has raised questions about the lines between military good order and discipline, and the legal rights of servicemembers as American citizens.

Merryday’s injunction is “an extraordinary intrusion upon the inner workings of the military” and has essentially left the Navy short a warship, according to a Feb. 28 filing by the government.

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“With respect to Navy Commander, the Navy has lost confidence in his ability to lead and will not deploy the warship with him in command,” the filing states.

The Navy has 68 Arleigh Burke-class destroyers in the surface fleet, 24 of which are based in Norfolk.

But while the government’s filing framed the judge’s order and the commander’s vaccine refusal as impacting the core of American military might, plaintiffs’ attorneys contend the case is ultimately about the rights afforded the plaintiffs under the Constitution and the Religious Freedom Restoration Act. That act bans the government from substantially burdening a person’s exercise of religion.

Navy officials declined to comment on the case or identify the commander or the ship he leads, but court records show the commander works for Capt. Frank Brandon, the commodore of the Norfolk-based Destroyer Squadron 26.

COVID commander

The Feb. 28 filing alleges that the commander has already disregarded Navy regulations after he “exposed dozens of his crew to COVID-19 when he decided not to test himself after experiencing symptoms.”

A declaration filed in early February by Brandon states he visited the Navy commander aboard his ship in November and that the ship CO “could barely speak.”

After a briefing involving dozens of sailors in close quarters on the ship, the Navy commander admitted to his boss that he had a sore throat.

Brandon ordered him to get a COVID test, and the commander tested positive after telling his boss he had discussed his illness earlier with the ship’s corpsman, according to the declaration.

The government’s Feb. 28 filing also argued that, even if the court found the CO credible, he can’t lead and crew a warship “given the breach of the relationships with both his commanding officer and his subordinates.”

A commanding officer can’t enforce orders to his 320-sailor crew if he does not abide by those orders himself, the filing argues.

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“By forcing the Navy to keep in place a commander of a destroyer who has lost the trust of his superior officers and the Navy at large, this Order effectively places a multi-billion-dollar guided missile destroyer out of commission,” defense attorneys wrote.

A Marine Corps lieutenant colonel tapped to lead a combat logistics battalion puts that service in the same boat, as “failure to follow the lawful policies and standards of her superio