WASHINGTON — The crew of the USS Theodore Roosevelt, sidelined in Guam with a coronavirus outbreak, is inching toward getting healthy and returning to sea duty while the fate of its former captain remains unclear.

The top Navy officer has recommended reinstating Capt. Brett Crozier, who was fired by the then-acting Navy secretary, but Defense Secretary Mark Esper wants more time to review the matter. When Esper would make a decision or whether the White House might get involved is unknown.

Meanwhile, most Roosevelt sailors are wrapping up weeks of quarantine as the ship prepares for its journey back to sea.

A look at what’s happening with the Roosevelt and what lies ahead:

A Recap

Crozier was fired on April 2 after sending an email to several naval officers warning about the growing virus outbreak on his ship and asking permission to isolate most of his crew on shore.

Acting Navy Secretary Thomas Modly said Crozier “demonstrated extremely poor judgment” and fired him. Modly then flew out to the ship and, in remarks to the crew, condemned Crozier, saying the captain may have been too naive or stupid to command the ship. Modly later apologized and resigned.

Adm. Mike Gilday, the chief of naval operations, met with Esper on Friday, laying out the results of a Navy investigation and his recommendation that Crozier return to the ship as captain.

The Captain

The return of the popular Crozier would boost the crew’s morale. It also would be a high-profile condemnation of Modly’s judgment. He was a political appointee of President Donald Trump but was never nominated to become the permanent secretary.

Trump has both criticized and empathized with Crozier, saying that he never should have written the emailed letter but that his career should not be destroyed for having “one bad day.”

Crozier, 50, is a 1992 graduate of the U.S. Naval Academy. He had been reported to have the virus but is thought to be recovering on Guam. His interim replacement, Capt. Carlos Sardiello, had previously commanded the Roosevelt but could head to a new assignment if Crozier returns.

The actions and judgment of Crozier are not the only issues Navy leaders have examined.

A preliminary inquiry conducted by the No. 2 Navy officer, Adm. Robert Burke, also considered a wider sequence of events that took place before the outbreak on the ship, including its visit to a Vietnamese port. It’s unclear whether the virus was picked up there or by other means such as air crews that operated off the carrier during its deployment. The Navy has said the decision to make the port visit was by Adm. Phil Davidson, head of the U.S. Indo-Pacific Command.

In Quarantine

More than 4,000 Roosevelt crew members have been moved ashore and are going through quarantine.

They’ve been prohibited from posting details about their confinement, but some sailors and their family members have talked freely about their quarantine in gyms, hotel rooms and other facilities around the island.

Sailors testing positive were put in gyms lined with cots, and they are checked by medical staff twice a day. Others are in hotel rooms set aside for the Navy, and public access is restricted. Internet access in some places can be spotty, and food was limited early on but has improved. Sailors read, watch movies and can walk around outside, as long as they stay within quarantine zones. Crew members communicate on a private Facebook page.

Getting the Crew Healthy

As of Monday, 955 crew members have the virus, one sailor is hospitalized and 14 have recovered.

Sailors must have two successive negative tests before they are considered virus-free. Only then could they begin moving back to the ship.

Crew on the Roosevelt have been cleaning the ship, space by space, and then cordoning off clear areas. No sailors have yet returned to the ship. They’ll eventually go back in large waves, go to clean sections and take over running the ship. Those who have remained on the Roosevelt to keep it secure and monitor its nuclear reactor will then go ashore for quarantine.

When the ship is deemed virus-free, it can then head back to sea.

Getting Underway

U.S. officials won’t say how long it will take for the ship to return to duty, but it has been docked in Guam for about a month and could be there another three to four weeks. To get back to sea, the ship will have to go through a regimented recertification process.

The flight deck — from the pilots to the crews and the system operators — has to be recertified. Pilots will have to log flight hours and conduct a certain number of takeoffs and landings from the carrier. Crews on the flight deck who direct the air traffic and those who operate the sensors and radars have to ensure everything runs right. Those checks could take several days.

The biggest question is where will the Roosevelt go. Originally it was slated to be at sea for months, then participate in a large Pacific naval exercise before heading home to San Diego.

Now Navy leaders have to decide whether to just send the beleaguered crew home or keep it out for a bit. The USS Ronald Reagan carrier strike group based in Japan could get underway in the coming weeks, as could the USS Nimitz, based in Bremerton, Washington.

The Nimitz pulled out for routine predeployment exercises Monday and likely will be out training for about a month.

And Then There’s the USS Kidd

As the Navy struggles to get one virus outbreak under control, another is bubbling up.

As of Monday, 47 sailors on the USS Kidd had tested positive, and Navy officials said the number was likely to rise. Two were evacuated to the U.S., and another 15 with symptoms were transferred to another ship for monitoring. The Kidd, a naval destroyer that had been doing counter-drug operations off South America, was expected to arrive in port at San Diego on Tuesday, a Navy official said.

The ship has a crew of about 350, and about 45% have been tested for the virus.