Trump looms large over an aircraft carrier's struggle with the coronavirus that has upended the Navy

• Acting Navy Secretary Thomas Modly resigned Tuesday amid the fallout over his handling of a coronavirus outbreak aboard the aircraft carrier Theodore Roosevelt.
• Modly has been widely criticized in recent days over his firing of the carrier's commanding officer and comments he made to the ship's crew justifying that decision.
• But behind the decision-making process, many see a Pentagon that is being bent to the whims of President Donald Trump.
• Visit Business Insider's homepage for more stories.

President Donald Trump has mostly remained in the background of events around the coronavirus-stricken aircraft carrier USS Theodore Roosevelt, but his handling of previous Navy scandals and attitude toward the Defense Department as a whole is shaping the decisions of department leaders, lawmakers and former officials say.

The saga of the aircraft carrier and Navy leadership began with the first positive tests aboard the ship and ignited when a letter from its commanding officer, Capt. Brett Crozier, pleading for help with the outbreak was leaked to the media.

It appeared to culminate with Crozier's firing on April 2, a decision Acting Navy Secretary Thomas Modly said he made because he lost confidence in Crozier and believed the captain "allowed the complexity of his challenge with the COVID outbreak on the ship to overwhelm his ability to act professionally."

Modly was widely rebuked for the decision and the message it sent.

John Kirby, a retired rear admiral and former State Department chief spokesman, tweeted that Modly's justification made it "hard to see it as anything other than an over-reaction & unwarranted at a vital time for the ship."

Trump's intervention in the case of disgraced Navy SEAL Edward Gallagher - reinstating his rank and preventing the Navy from removing his SEAL qualification - eventually led to the resignation of Modly's predecessor, Richard Spencer, also loomed over the Crozier firing, according to Lindsay Cohn and Alice Friend, both professors, and Jim Golby, an Army officer advising the US mission to NATO.

Neither Trump's nor Modly's authority to make those decisions is in question, they wrote in a Washington Post opinion column. But, in Modly's case, "the fact it was a political appointee associated with another highly politicized case who relieved Crozier, rather than a uniformed officer in the chain of command, may contribute to a perception that this is more about political embarrassment than a breach of security."

'In the president's shoes'

Over the weekend - when Trump broke his silence on the incident to criticize Crozier's letter - Modly admitted to making the decision with Trump in mind, telling Washington Post columnist David Ignatius on Sunday that he didn't want the president to "feel that he had to intervene because the Navy couldn't be decisive."

"I put myself in the president's shoes," Modly told Ignatius. "I considered how the president felt like he needed to get involved in Navy decisions" regarding Gallagher and Spencer. "I didn't want that to happen again," Modly added.

Crozier's firing "comes from the top," Ray Mabus, Navy secretary during the Obama administration, tweeted on Sunday. "We have a [commander-in-chief] who pardons convicted war criminals, calls people "my generals' ... Firing [the commanding officer] sends chilling signal to other commanders."

Many lawmakers also inveighed against Modly after the Crozier's firing, including the chairman of the House Armed Services Committee, Rep. Adam Smith, and the chairs of HASC's subcommittees, who called it "a destabilizing move" likely to put service members and military readiness at risk.

On a conference call Tuesday, hours before Modly's resignation, Smith pointed to that Washington Post interview as a sign of Trump's influence, saying Modly's decision was indicative of a leadership style "that basically says facts don't matter, competence doesn't matter, getting the job done doesn't matter. All that matters is that you praise the president 24/7."

"When you start trying to run an operation based on that premise, I mean, you're going to make incompetent decisions like we saw play out with the Roosevelt," Smith added.

Smith emphasized that he thought "very highly" of Modly and Defense Secretary Mark Esper, "in terms of their dedication, their skill, their competence, and their ability."

"What I see here is what you would call undue command influence. I see the creeping influence of Trump's approach undermining the decision-making process within DoD," Smith said.

'You are justified in being angry'

Smith said he was "not unsympathetic" to Esper and Modly, as Trump is at the top of the military chain of command.

"But I am very, very worried about the impact that it's having on their decision making," Smith said. "When I listened to the speech that acting Secretary Modly gave, it was almost like he was trying to do sort of a half-ass imitation of how Donald Trump would have given a speech. It wasn't what I would've expected from the Thomas Modly that I know."

"Why would a competent, capable veteran who has expensive experience, extensive leadership skills make what seems like such an obvious mistake?" Smith added. I think it's because everyone [in the Pentagon] is trying to figure out, how do I stay in the good graces of the tyrant across the river there, who could potentially fire me tomorrow if I don't?"

In his resignation letter, Modly thanked Esper and Trump for their "confidence." In a memo to the force, Modly apologized for a "lack of situational awareness" during an address to the crew on Theodore Roosevelt on Monday that provoked a firestorm off the ship.

"You are justified in being angry with me about that," Modly wrote, according to Task & Purpose. "There is no excuse, but perhaps a glimpse of understanding, and hopefully empathy."

During a press conference Tuesday evening, Trump said he had "no role" in Crozier's firing but again criticized him over the leaked letter, saying Crozier "didn't have to be Ernest Hemingway."

Modly "probably shouldn't have said quite what he said, but he didn't have to resign," Trump added. "But he felt it would be better for the country, so, you know, I think it will end quickly."

Do you have a personal experience with the coronavirus you'd like to share? Or a tip on how your town or community is handling the pandemic? Please email covidtips@businessinsider.com and tell us your story.

And get the latest coronavirus analysis and research from Business Insider Intelligence on how COVID-19 is impacting businesses.