“This is one of the toughest decisions I have ever had to make. Thank you for an incredible journey and for the support you have shown me,” Long wrote in a lengthy farewell letter emailed at 3:12 p.m. to FEMA staff.

Long clashed with his direct superior, Homeland Security Secretary Kirstjen Nielsen, in September, when Nielsen appeared intent on forcing Long out of his job even as Hurricane Florence dumped historic amounts of rain on the Carolinas. The relationship deteriorated when an internal investigation became public. The Homeland Security inspector general looked into Long’s use of government vehicles to travel between Washington and his home in North Carolina.

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In the middle of the storm, Long told colleagues at FEMA he was on the verge of quitting. But he was popular in the agency and stayed on — until Wednesday, when he surprised his colleagues with his decision to leave.

In an interview with The Washington Post in September, Long called his relationship with Nielsen “professional and functional” and added, “We both understand what needs to be done.” But behind the scenes, Nielsen was irritated with Long for not attending early-morning meetings with top-level DHS staff, and she disapproved of his absences from Washington when he visited his family in North Carolina, an administration official said in September.

The FEMA administrator has an unusual role. FEMA is part of Homeland Security, so Nielsen was Long’s boss, but a FEMA administrator simultaneously has authority to offer advice directly to the president during disasters. This competing chain of command contributed to the friction between Nielsen and Long, several current and former administration officials said.

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Long, who had many years of experience in emergency management, easily won Senate confirmation when nominated to the FEMA post two years ago. He quickly had his hands full when Hurricane Harvey slammed into Texas and dropped multiple feet of rain, flooding Houston and killing dozens of people. That was soon followed by two more major hurricanes, Irma and Maria, and then controversy over the administration’s response to Maria, which left a death toll in Puerto Rico estimated at nearly 3,000.

Last year saw two more epic hurricanes, Florence and Michael, and fatal wildfires in California.

“No one could have ever predicted the challenges we would face. Over the past two years, we led this Nation through the toughest series of disasters ever experienced — our mission spanning half the globe,” Long wrote in his farewell letter.

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He also had to handle internal agency problems. He launched a campaign against sexual harassment, dubbed “Not on My Watch,” in which he promised to eradicate what he called a “culture” of misconduct he said has persisted at FEMA for years. In August, he revealed misconduct allegations against the agency’s former personnel chief, who Long said was preying on female employees and in some cases transferring them to different offices to be near male staffers.

Meanwhile, Long became mired in the controversy over his use of government vehicles. Long’s improper use of government resources cost taxpayers $94,000 in staff salary, $55,000 in travel expenses and $2,000 in vehicle maintenance, the DHS inspector general determined. FEMA officials have said that Long repaid the money and took corrective steps in recent months to resolve the issue, which stemmed from the long-standing practice of FEMA administrators traveling in vehicles equipped with emergency communications gear.

An agency spokeswoman said Wednesday that his departure was unrelated to the vehicle controversy.

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“It honestly has nothing to do with the travel issue. He’s been away from his family for a long time,” said Lizzie Litzow, the FEMA press secretary. “And he’s chosen this moment to make sure the new administrator has enough time to prepare for upcoming hurricane season before it hits.”

Long’s departure had the agency buzzing Wednesday.

“He took the travel issue so personally that he never got over it,” said one FEMA official, who spoke on the condition of anonymity because the official was not authorized to speak to reporters.

The FEMA official said Long’s reputation remained strong among FEMA staffers, many of whom believe he was forced out by Nielsen’s office. “There’s no question they wanted him out,” the official said, “but whether he was forced out or decided to quit is difficult to pinpoint.”

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A DHS official who works closely with Nielsen and who had spoken to Long rejected the claim that Nielsen wanted him out.

"We were surprised by this. We wanted him to stay, but the guy’s burned out. He’s exhausted,” said the official, who spoke on the condition of anonymity to describe DHS personnel moves.

“Everybody likes the guy. He was good on TV,” the official said. “We didn’t think the car thing was a big deal.”

The investigation last fall blindsided Long right at the moment he was coping with Hurricane Florence in his home state of North Carolina. Long had begun a signature project in the aftermath of the storm, embedding small groups of FEMA employees inside state agencies to create a more seamless response to the natural disaster. In an interview with The Post during the Florence response, he recalled that the first storm he ever lived through was Hurricane Hugo, in 1989, when he was 14 years old.

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“We had numerous trees down our yard. I think there were eight just across our driveway, no power for roughly 10 days, and I was out of school forever. And you know, I think that that could have been a catalyst that got me really interested in disasters,” he said.

Asked about the controversy over his use of a government car, he said, “I walked to work. I’ve been bitten by a dog walking to work. I’m not even offered a parking spot in my own headquarters. So what’s being put out there, it’s far from the reality.”

In his farewell letter, Long wrote: “While this has been the opportunity of the lifetime, it is time for me to go home to my other family — my beautiful wife and two incredible boys. Life is too short not to be with the ones that you love most, and I need to ensure my boys grow up to exhibit the same levels of patriotism that you do. With that, I have respectfully resigned as FEMA Administrator.”