On Thursday, the Navy relieved Capt. Brett Crozier, commander of the nuclear-powered aircraft carrier USS Theodore Roosevelt, after the San Francisco Chronicle obtained and published a letter he wrote asking his Navy superiors to evacuate and quarantine most of the sailors on board. Crozier’s letter came after covid-19 infections began to spread on the Roosevelt, with three cases on March 24 escalating to over 100 positive cases as of April 3.

The Roosevelt’s crew of nearly 5,000 gave Crozier a rousing send-off. Since being relieved of command, Crozier has been hailed as a hero by many, while the Navy has maintained his handling of the letter led to a loss of trust and confidence in his leadership.

Here are three things to know about this case.

1. Military commanders get removed, but this is an unusual situation

After the initial three sailors tested positive for coronavirus and were medically evacuated from the ship, Acting Secretary of the Navy Thomas Modly stated this demonstrated the U.S. ability to keep the Navy’s ships fully functional while dealing with the pandemic. But Capt. Crozier argued that this conservative approach endangered the health and lives of his crew and that the Navy should remove most sailors from the ship (leaving a skeleton crew to manage the reactor) and into quarantine while the ship was thoroughly cleaned. On March 28, Crozier wrote a letter to his superiors making his case, sending the letter over unclassified email and reportedly copying individuals not in his chain of command. The letter then appeared in the San Francisco Chronicle on Tuesday.

At first, both the Navy’s military chief Admiral Michael Gilday and civilian Acting Secretary Modly stressed Crozier would not face “any type of retaliation” for having written the letter to his chain of command. On Wednesday, the Navy began evacuating more sailors from the ship. Then, on Thursday, the news media reported the Navy would relieve Crozier of command after all.

It is normal for military commanders to be relieved of duty for losing the “trust and confidence” of their superiors. Civilian leaders have relieved commanders over public disputes before — as was the case in 2010 for the commanding general of the war in Afghanistan, Stanley McChrystal.

Here’s what’s unusual in this case: As military ethicist Pauline Shanks Kaurin has argued, members of the military are subject to multiple, sometimes competing, loyalties. Unlike most cases of poor judgment or policy disagreement, this case involves an officer who believed he had to choose between loyalty to his people and loyalty to the rules of his organization. The military leadership appears to be saying Crozier showed poor judgment in privileging his loyalty to his people over loyalty to the institution.

2. Health and military readiness are intertwined

Public statements by Navy leaders suggest they are attempting to strike a balance between managing the spread of covid-19 among sailors and keeping ships operating as normal.

But this framing suggests a false choice. Military readiness depends on the health of the force. All four branches of the U.S. armed services frequently state people are their most valuable asset, and two Army generals are being praised for their pro-active measures that appear to have kept their people safe.

Nevertheless, analysts suggest the armed forces struggle with an underlying culture of not admitting to shortfalls. As a result, commanding officers feel pressure to claim full readiness on paper — despite any concerns over the health, welfare and therefore the actual readiness of their people.

The Navy is no stranger to this problem. In 2017, independent analysis found the Navy systematically suppressed complaints about gaps in personnel and other challenges before two major collisions at sea. One of the findings of the report was that communication between ship commanders and Navy leadership had broken down.

3. The Crozier case exposes challenges in the Navy’s command structure

Modly’s April 2 Defense Department briefing suggests he lost trust and confidence in Crozier because he believed the captain exercised poor judgment in widely disseminating a letter that might cause panic or reveal specific weaknesses to adversaries.

In his official statement, Modly insisted his message isn’t that the Navy does not want to hear bad news — just that it needs to come through the proper channels. Of course, all militaries depend on respect for the chain of command to ensure proper communication, discipline and coordination.

But that message may be lost upon many. Both the public response and the response among Navy personnel has been largely negative. The House Armed Services Committee leadership released a joint statement criticizing Modly for the decision, and Defense Secretary Mark T. Esper for taking a hands-off approach. A group of U.S. senators followed suit.

Democratic presidential front-runner Joe Biden condemned the Navy leadership in a tweet. Retired rear admiral and former Pentagon spokesperson John Kirby called the firing “reckless and foolish.” And retired Adm. Mike Mullen, the former Chairman of the Joint Chiefs of Staff, said relieving Crozier of command “was a really bad decision.”

President Trump, who had not commented during the week, broke his silence Saturday, saying Crozier’s letter was “not appropriate” and insinuating Crozier was responsible for exposing his sailors to the virus by making a stop in Vietnam — a stop that was pre-scheduled by the regional command in charge of the Pacific.

Also complicating the optics of the situation is the involvement of Modly himself. Last summer, Trump intervened in the Navy’s handling of a personnel action involving Chief Petty Officer Eddie Gallagher, ultimately resulting in the November 2019 removal of then-Secretary of the Navy Richard V. Spencer and the installation of Modly as acting secretary. While no one disputed the president’s legal authority, many questioned the appropriateness of civilian political intervention into internal professional processes. Similarly, no one questions Modly’s legal authority to remove a commander in whom he has lost confidence. But the fact it was a political appointee associated with another highly politicized case who relieved Crozier, rather than a uniformed officer in the chain of command, may contribute to a perception that this is more about political embarrassment than a breach of security.

Command of a ship is an unforgiving job, but so is political leadership of the Navy. Crozier may be gone, but two major leadership scuffles within the past year suggest the Navy’s problems are not over.

Lindsay Cohn is an associate professor of national security affairs at the Naval War College.

Alice Friend is a visiting research professor at the U.S. Army War College and a Senior Fellow at the Center for Strategic and International Studies.

Jim Golby is an Army officer serving as a defense policy adviser at the U.S. mission to NATO.

The opinions expressed here are those of the authors and do not reflect the official position of the Naval War College, the Department of the Army, the U.S. Mission to NATO or the Department of Defense.