Chief of Naval Operations Adm. Michael Gilday reversed course and said Friday the U.S. Navy will not reinstate Capt. Brett Crozier to command the aircraft carrier USS Roosevelt, after he wrote a letter warning about the coronavirus outbreak aboard the ship. The letter was later leaked to the San Francisco Chronicle.

After a formal investigation, Gidlay changed his mind about reinstating Crozier upon learning more details about what led to 1,200 of the 5,000 sailors aboard the ship testing positive for COVID-19, the Navy announced Friday.

In addition, the promotion of Capt. Crozier’s commanding officer Rear Adm. Stuart Baker to two-star admiral will be delayed.

Gilday learned “following the finding of facts” that Crozier “did not meet the standard expected for a commanding officer,” a senior defense official told Fox News.

NAVY OPENS FULL INVESTIGATION INTO CORONAVIRUS-STRICKEN USS ROOSEVELT

Crozier was fired April 2 by then-acting Navy Secretary Thomas Modly after sending a message to several naval officers warning about the growing virus outbreak and asking for permission to isolate the bulk of his crew members onshore in Guam, where the ship was forced to dock due to the outbreak. It was a bold move that would take the carrier out of duty in an effort to save lives.

“If we do not act now, we are failing to properly take care of our most trusted asset – our sailors,” Crozier stated in his letter, which was published by the San Francisco Chronicle. The investigation did not conclude that Crozier leaked the letter to the media.

Following Crozier’s dismissal, the crew of the USS Roosevelt gathered in the ship’s hangar deck to cheer for and applaud their captain. The send-off was captured on video and shared across social media.

Modley resigned from his position one day after he apologized for suggesting the ousted commander of the Roosevelt was either "too naïve or too stupid" -- or perhaps even deliberately insubordinate -- over his handling of the ship's coronavirus outbreak.

NAVY RECOMMENDS REINSTATING OUSTED USS THEODORE ROOSEVELT CAPTAIN

The Navy stressed Crozier was not released from duty for the email or for firing the red flare about the outbreak on his ship.

However, the Navy concluded that Crozier had multiple opportunities to alert his chain of command to his concerns before writing the leaked email. Also on the email he only addressed fellow aviators, leaving off a key submariner who was in his chain of command.

Rear Adm. Baker as well did not voice his concerns up his chain of command, according to the defense official. “They did not get people off the ship fast enough. They chose comfort over safety.”

The investigation found that upon learning that coronavirus had made its way onto the ship when it was forced to dock in Guam, COVID-positive sailors did not depart the ship expeditiously and Crozier did not enforce social distancing on the ship.

Crozier chose “the comfort of his sailors” over quickly offloading them from the ship because there were not comfortable hotel rooms immediately available, according to the official.

He also released those from quarantine prematurely who said the berths onboard were not comfortable enough, thus contributing to the spread of the virus.

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Crozier eventually tested positive for coronavirus and he was captured on shaking hands with sailors on shore after being fired and leaving the ship, against CDC protocol.