The Navy has sent an aircraft carrier that was crippled in port for two months with a coronavirus outbreak back to sea, as officials acknowledged that new cases of the disease could arise on the ship.

The USS Theodore Roosevelt departed Naval Base Guam on Thursday, in anticipation of needed qualifying landings for pilots on the 1,093-foot ship. The Navy’s top officer, Adm. Mike Gilday, asked how he could be confident there will not be an additional outbreak aboard, asked for a different perspective.

“I would ask you not to look at every covid case on every ship as a failure,” Gilday responded in a phone call with a handful of reporters.

The carrier, with a crew of about 4,900 sailors, is returning to sea after the virus first appeared on the ship in March and rapidly spread through the crew. The ship pulled into port in Guam at the end of the month, and more than 1,100 sailors eventually tested positive, including one who died.

Gilday acknowledged 14 sailors who previously tested negative for the virus developed flu-like symptoms after returning to the ship and have been placed in quarantine again. The Navy, he said, is still understanding the incubation period for the virus and is preparing for the possibility of dealing with the coronavirus beyond 2020.

“We’re just planning for the worst, really,” Gilday said. “We have to be ready to continue to operate regardless of the levels of covid.”

Gilday said a few hundred sailors from the Theodore Roosevelt’s crew are still in Guam recovering from the virus, and Navy officials are working to understand when those individuals are no longer contagious. Some of those sailors will rejoin the ship after the aircraft qualifications are complete in a few days, he said.

Gen. David Berger, the commandant of the Marine Corps, said in the same phone call that he and other members of the Joint Chiefs of Staff met on Monday with Anthony S. Fauci, the nation’s top infectious-diseases expert, and Deborah Birx, the White House coronavirus response coordinator. It is hard to predict whether the United States will be hit with another wave of coronavirus infections, he said.

“There is too many unknowns, from their perspective, to accurately forecast,” Berger said. “Although, clearly, we’ve learned a whole hell of a lot from the last three, four months, should that happen.”

Berger said military leaders are not talking about a “post-covid era,” but looking at the issue as “a continuum, where we need to make adjustments along the way.”

“The military is not a work-from-home force,” Berger said. “You expect us to be out there. You expect us to figure out how to do that safely, and that’s what we’re going to do.”