The decision not only delays Crozier's potential return by at least a month, but it also opens the possibility that the earlier recommendation to bring him back on board could be overturned, according to a senior defense official.

The controversy over the captain, who in late March wrote a letter pleading for help from Navy leadership as coronavirus spread throughout his ship and was later fired when the memo was leaked to the media, appeared to be simmering down last Friday when senior Navy leaders recommended to Defense Secretary Mark Esper that Crozier be reinstated as captain.

At the time, Joint Chiefs Chairman Gen. Mark Milley advised Esper to defer a decision and instead open a fuller investigation into the matter, POLITICO first reported.

Milley's advice to Esper was "to ensure that the inquiry was as thorough as it needs to be to answer any questions the secretary may have had before finalizing the report," said one defense official. POLITICO previously reported that Milley was not against Crozier being reinstated; just that a larger investigation should be conducted.

McPherson — who initially agreed with Gilday that Crozier should be reinstated after the preliminary inquiry — changed his mind after hearing Milley's advice, the senior defense official told POLITICO. While Milley is not in the chain of command, he is the principal military adviser to President Donald Trump and Esper.

The White House has not yet weighed in on the case, despite Trump's suggestion that he might intervene, the official said.

House Armed Services Chairman Adam Smith (D-Wash.) told reporters he spoke with McPherson on Wednesday morning and again called for Crozier’s reinstatement.

“I do think it’s perfectly legitimate to extend the investigation about everything that happened with the Roosevelt,” Smith said. “I think a forensic analysis of that is enormously important and I completely agree that that’s not something you can get done in a week.

“However, on the question of whether or not Captain Crozier is the right person to continue the command that they gave him in the first place, I believe that question should’ve been clearly answered to this point,” Smith said. “From everything that’s come out and everything I’ve seen, there was no reason to relieve him of his command.”

The move is the latest in a highly publicized chain of events that started with an outbreak of the coronavirus onboard the Roosevelt in late March, which forced the ship to stop in Guam and offload its 5,000 sailors. Former acting Navy Secretary Thomas Modly fired Crozier after his memo pleading for help combating the virus leaked to the media. Modly later resigned over remarks he made to the ship's crew criticizing the captain's actions.

Smith cited reports that Modly fired Crozier because the acting secretary assumed that's what Trump wanted.

“I do not want to see the Department of Defense become yet another aspect of our federal government that the Trump administration has brow beaten into the position where they view their job as solely consisting of making sure that they’re kissing up to the president of the United States," Smith said.

“I don’t want DoD to lose the competence that they have and simply become yet another organization whose job it is to pump up the president’s ego," he said. "A way they could make a strong statement that that’s not where they’re going is to give Captain Crozier his job back."

Sailors head back on board

Although he was removed from command, Crozier remains in Guam as he recovers from Covid-19. As of Tuesday, the Navy reported 940 active coronavirus cases among the crew, and 29 recovered. One sailor has died.

The Navy began moving hundreds of sailors back onto the Roosevelt Wednesday as the ship prepares to return to sea, the service announced. In order to go back on board, sailors must have completed their period of quarantine or isolation and tested negative for Covid-19 twice.

The crew will return to the ship in waves, starting with those responsible for "critical services," according to a Navy statement. In the meantime, the 700 sailors who stayed onboard to clean and run essential services since the ship docked in Guam on March 27 will now begin their isolation.

Once onboard, the crew must all wear masks and other personal protective equipment, and must follow other Covid-19 prevention protocols such as social distancing.

The sailors will be given a mask before even leaving isolation and will have to wear them every day for the rest of the deployment, other than while eating, sleeping and showering, one sailor said.

Connor O'Brien contributed to this report.

