The situation was so dire on the USS Theodore Roosevelt that by March 30 leaders on the coronavirus-stricken aircraft carrier found themselves “inside a tornado fighting a war,” according to emails recently released to Task & Purpose by the Navy.

The Navy handed over 200 pages of email communications this week in response to a Freedom of Information Act lawsuit filed by Task & Purpose in April. More than 1,000 additional pages remain under review, Navy officials said.

The emails shed new light on the unprecedented outbreak of novel coronavirus (COVID-19) on the aircraft carrier following a port visit to Vietnam in early March, while offering a window into the intense pressure placed on the ship’s commanding officer, Capt. Brett Crozier, in the days before he pleaded with Navy officials to get all of his sailors off the ship as the virus continued to spread like wildfire.

“We are not at war. Sailors do not need to die. If we do not act now, we are failing to properly take care of our most trusted asset — our Sailors,” Crozier, 50, wrote in a four-page letter to senior Navy leaders on March 30. The letter was leaked and published the following day by The San Francisco Chronicle.

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The outbreak would ultimately infect 1,273 sailors out of the roughly 5,000 sailors on board the ship, one of whom died from the disease: Chief Petty Officer Charles Robert Thacker Jr. At one point during the outbreak, the aircraft carrier’s medical team estimated that 50 of the crew could die from COVID-19, a Navy investigation determined.

By the time Crozier’s letter had become public, the crisis was already spiraling out of control. The ship’s senior medical officer, Capt. John York, on March 24 reported just three positive cases on board that were in the process of being medically-evacuated. But infected sailors, many showing no symptoms, continued to spread the virus despite a so-called “bleachapalooza” cleaning effort, according to the emails.

“This will become a testing problem very quickly,” York warned in another email sent hours later to the strike group commander, Rear Adm. Stuart Baker, who was also onboard the ship and receiving regular updates from the medical officer with Crozier copied.

That morning, a petty officer from the ship’s reactor division, a crucial section that operated its nuclear propulsion system, had come down with body aches, sore throat, and a 101.4-degree fever. In the email to Baker, York confirmed the sailor had tested positive, putting hundreds of sailors critical to the ship’s function at risk.

“The potential operational impacts of quarantining this large group is obviously significant,” York wrote, adding that Crozier and other leaders were aware.

“This was a hugely complex issue and no one had a playbook for it,” Adm. John Aquilino, the four-star commander of U.S. Pacific Fleet, later told investigators. “No one knew at the time about the extent of the asymptomatic spread challenge with this virus.”

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The next day, York reported that 23 sailors tested positive. At least 750 sailors had had “close contact” and were in danger of contracting the virus: “Expect it will continue to grow, possibly getting close to 1000.”

“Regardless how long this will take to get a ‘healthy’ ship, in order to go out to sea – all current models are based on knowing when the first patient started infecting others and that the ship doesn't pull into port, and they show the disease lingering through the crew for almost a year,” York wrote in a March 25 email, stating that he was operating in the “fog of medical war.”

“Our situation is very different in that we (and the infectious disease experts back home) are now assuming that all the patients we're seeing are effectively the second or third generation of patients,” York added. “Best estimate right now based, with our plan for strict quarantine of all close contacts, is that we may be ‘healthy’ in 60 days. More models to be run in the coming days.”

York projected that by the next evening, the ship would have 50 positive cases and 1,500 close contacts. It was obvious that the ship’s cramped passageways and tight living quarters made social distancing impossible. Meanwhile, a quarantine area established in the ship’s aft had become the site of “true human suffering” where close quarters and lack of food among the sick were the norms, the ship’s executive officer later told investigators.

“I regret attempting [the aft quarantine] and would not do it again,” Capt. Daniel Keeler said. “By the time we pulled into Guam, it was apparent the entire ship met [the Navy’s] definition of ‘close contact.’”

By mid-day on March 26, York, the senior medical officer, reported more than two dozen sailors testing positive, then 38 by March 27. And the numbers continued to climb with each passing day: First to 44, then 53, then 85. By April 1, it was 162.

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Meanwhile, family members of the sailors were becoming increasingly worried. The ship’s ombudsmen team, which provides official updates to families of the thousands of sailors on board, emailed Crozier directly on March 26 to tell him that family members were concerned they were not being provided timely information. Multiple reports had come in, the ombudsman wrote, that sailors in quarantine were still standing watch, eating in the ship’s galley, and using computers while awaiting test results.

“General mistrust will be multiplied exponentially,” the ombudsman wrote, mentioning a Navy Times article published that morning reporting the ship would be pulling into Guam until further notice and have the entire crew tested. “With this particular article, and with the general message we have been putting out, the optics do not look great.”

Would sailors be allowed off the ship? What safety measures are being implemented? asked the ombudsman team, echoing questions raised by family members. A response from Crozier was not included in the emails released to Task & Purpose.

But those questions were clearly weighing on Crozier, who later estimated that he was getting just four to five hours of sleep a night after the outbreak began. If nothing was done, he believed, at least five or six of his sailors were going to die if “we didn’t take immediate decisive action,” he told investigators.

Some in Crozier’s command, though well-intentioned, were moving too slowly and focused on bureaucratic minutiae, he said, like debating whether to put Social Security numbers on testing kits. Crozier wanted the focus to be on what he thought was best: getting sailors off the ship and into individual isolation in hotel rooms in Guam, instead of ad hoc and largely ineffective group living quarters that had been established in gyms and shared barracks ashore.

“CO, [command master chief], and I are inside the tornado fighting a war,” wrote Keeler, the executive officer, in an email sent on March 30.

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Still, Crozier told investigators he was expecting a phone call on March 28 from Adm. Michael Gilday, the chief of naval operations. It was canceled for reasons unknown to him, he said.

“The phone call might have provided a more thorough understanding of wider Navy efforts to combat the virus onboard and with our crew, allowed me to communicate our desire to get sailors into effective isolation quarters ashore, and instilled confidence that the situation was being rapidly addressed at the appropriate levels,” Crozier told investigators.

The ombudsman team again wrote Crozier on March 30: “We are receiving multiple emails from families that are detailing some very concerning living conditions for sailors who have tested positive for COVID 19.”

“Namely, the overwhelming lack of medical treatment or check-in for sailors who have been moved off the ship. Basic living necessities are also an issue, whether it be medicine, toiletries, etc. There are also sailors experiencing symptoms who seem to not be receiving care. We are all very concerned for our sailors and their families at this time, but we need to be able to reassure our families that their sailors will be taken care of, not forgotten about. This influx of emails and questions are alarming.”

That same day, an email hit the inboxes of a number of senior Navy officers. It was from Crozier. Under the subject line, “TR request for assistance,” Crozier wrote that he had lost confidence in the normal processes used in response to the virus and suggested that their current efforts at containment pier side in Guam were “inadequate.”

“I fully realize that I bear responsibility for not demanding more decisive action the moment we pulled in, but at this point, my only priority is the continued well-being of the crew and embarked staff,” Crozier wrote in the March 30 email.

“As you know, the accountability of a Commanding Officer is absolute, and I believe if there is ever a time to ask for help it is now regardless of the impact on my career,” he concluded, also attaching a four-page letter in which he said keeping 4,000 young men and women on board the Theodore Roosevelt was “an unnecessary risk” that “breaks faith with those sailors entrusted to our care.”

“He would not have sent this letter if he knew hotel rooms were coming soon,” Keeler, his second-in-command, told investigators.

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By March 31, the situation had grown so chaotic that an unknown person tried to book 400 hotel rooms on Guam for the ship's crew. In an email forwarded to Crozier and Baker that day, a member of the Marriott sales team in San Diego, the ship’s homeport, advised that sailors could only check into a hotel after testing negative for COVID-19 due to an executive order from Guam's governor.

“Apparently somebody has been calling to look for large numbers of hotel rooms in Guam for TR,” one officer wrote in a March 31 email to Baker and Crozier.

The following day, Keeler passed along a pre-decisional document and other information and then added, “Let me know if this answers the mail as far as convincing the hotels we are not looking for a party.”

Crozier told investigators that he was sending up a “red flare” for help and mentioned that flag officers had always urged him to reach out if he ever needed help. He knew the admirals were “biased towards action, [could] make quick decisions, and … could solve the problem on behalf of the sailors,” he said.

“I’m going to get fired for this,” Crozier said after he sent the letter, recalled Capt. Steve Jaureguizar, the commander of the carrier’s air wing, in a statement to investigators. “I replied, ‘I don't think so – you have a responsibility to get [the] necessary information to senior leadership.”

Then, on March 31, five senior medical officers wrote and signed their own letter recommending that all sailors be removed from the ship, and threatened to make the letter public, according to a timeline from U.S. Naval Institute News. Meanwhile, a San Francisco Chronicle reporter had a copy of Crozier’s letter and was reaching out to the Pentagon for comment. An article based on the document was published later that day.

“While all the warfare commanders felt the right information had been provided to the chain of command and up the chain of command, there was an apparent disconnect somewhere,” Jaureguizar said. “I believe Captain Crozier thought critical information was not getting to who it needed to get to via that method, and there was no more time [to] keep attempting the same prior route.”

Navy officials secured 4,000 hotel rooms to quarantine sailors on Guam on April 1. The next day, citing “extremely poor judgment,” Acting Navy Secretary Thomas Modly launched an investigation and immediately relieved Crozier of command, which Keeler, the executive officer, later described as “dropping a nuclear bomb in the middle of an ongoing crisis.”

(Modly himself would resign a week later after traveling to Guam to address the crew, calling Crozier “too naive or too stupid to be a commanding officer” of their ship since the letter he wrote to Navy leadership subsequently leaked to the press. Audio of Modly’s remarks quickly leaked to the press).

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“I asked him why he sent [the letter] without talking to me first and he said that he didn't tell me because he thought I would try to talk him out of sending it,” Rear Adm. Baker later told investigators, adding that he was “surprised and angry” Crozier had done so.

“If Captain Crozier had presented it to me before he sent it, I would have had a conversation about why it is not a proper way to handle this type of action and I would tell him the proper way was to go to my boss, the 7th Fleet Commander, which is what we were already doing,” he added. “My frustration was that I didn't understand what he intended to gain from that letter because Captain Crozier knew these [courses of action] were being worked.”

Many of the sailors under Crozier’s command, however, saw things differently. As Crozier walked off the ship for the last time, thousands clapped and cheered, “Captain Crozier! Captain Crozier!” And an online petition to have him reinstated garnered more than 500,000 signatures.

“Whether you intended for your letter to be made public or not is beside the point,” one Navy commander, their name redacted in the released emails, wrote Crozier on March 31. “You are a HERO for looking out for your sailors and I’m sure they are grateful for it. We need more leaders like you in our Navy.”

That same day, a commanding officer from a warship with Naval Surface Force Atlantic, wrote Crozier to thank him.

“I wanted to say thank you for your letter and your taking the risk to help your sailors,” the unnamed commander wrote. “I had my first positive COVID 19 onboard this morning and while trying to lead 300+ in a tough time I was subsequently being questioned by [Commander Naval Surface Force Atlantic] along the lines of how could I let this happen.

“CNSL has mirrored most of Navy leadership in trying to wish this problem away and I thought your letter was spot on in trying to preserve readiness by preserving our force,” the officer added, saying that he was currently being quarantined along with more than 40 crew members.

“The response from CNSL and [U.S. Fleet Forces Command] took a step change about mid-afternoon, right around when your letter hit major news sources … Thank you for having the guts to do what you did today sir. I can tell you there are a number of us at the O5 level that feel like we are being second-guessed in any action taken to prevent this from taking over as well as our response. Hopefully, your letter starts to move the needle in how we are dealing with this onboard ship and the Navy writ large.”

Indeed, the Navy learned a great deal from the outbreak on the Theodore Roosevelt and other ships but ultimately decided not to reinstate Crozier to command, effectively ending his career. Crozier’s letter was “unnecessary,” Adm. Michael Gilday said in June.

But many of the people who served alongside Crozier maintain that he did the right thing to protect his sailors’ lives amid an unprecedented crisis.

“I believe he always had [the] crew’s best interest in mind,” Capt. John York told investigators in May, recalling Crozier’s first meeting with department heads on the ship.

“He said, ‘in every decision you make, you need to take into account how it would affect sailors because sailors are the most important thing.”

AUDIO: Acting Navy Secretary Thomas Modly addresses crew of USS Theodore Roosevelt