Former pilot who allegedly threatened to shoot flight captain once sued DOD against Covid-19 mandate

The former Delta Airlines pilot who was indicted for allegedly threatening to shoot a flight’s captain mid-flight is an Air Force reservist who previously sued the Department of Defense over Covid-19 vaccine requirements for service members. 

Jonathan J. Dunn served active duty for the Air Force from 2003 to 2014. He entered Air Force Reserves Service as a generalist pilot in November 2000 and has completed “20 years satisfactory service,” a spokesperson for the Air Force told NBC News.

This week, the U.S. Department of Transportation’s Office of the Inspector General announced that Dunn was indicted by a grand jury in the U.S. District Court for the District of Utah on Oct. 18 for interfering with the crew of a commercial airline flight. 

In that incident, which unfolded Aug. 22, 2022, Dunn was the crew’s first officer when he allegedly got into a “disagreement” about a “potential flight diversion due to a passenger medical event.”

He allegedly “told the captain they would be shot multiple times if the captain diverted the flight,” the Office of the Inspector General said. Dunn was authorized to carry a firearm via the Transportation Security Administration’s Federal Flight Deck Officer program, meant to defend the flight deck against criminal violence or air piracy. 

Dunn has since been removed from that program, the TSA said, and is no longer employed with Delta. 

A two-page indictment said Dunn “did assault and intimidate a crew member of an aircraft, thereby interfering with the performance of the duties of the crew member and lessening the ability of the crew member to perform those duties, and did use a dangerous weapon in assaulting and intimidating the crew member.”

The Air Line Pilots Association said in a statement: “The safety and security of our crews and passengers is our highest priority, and this individual’s action is wholly inconsistent with that mission.”

Dunn’s initial appearance and arraignment is set for Jan. 4. NBC News has reached out to an attorney listed for him.

Dunn could not be immediately reached for comment Friday.

Dunn, a lieutenant colonel in the Air Force, had filed a lawsuit in February 2022 against the Department of Defense, Secretary of Defense Lloyd J. Austin, Air Force Secretary Frank Kendall, and two of his commanding officers to avoid punishment for refusing to get the Covid-19 vaccine, according to a source familiar with the matter and court records.

According to that suit, he last lived in Marysville, California, flew combat missions over Afghanistan, and in August 2021, took command of the 452 Contingency Response Squadron in California.

The complaint cites Secretary of Defense Austin’s memorandum issued Aug. 24, 2021 requiring all service members be vaccinated. (The Pentagon later dropped that policy in January). The complaint said Dunn was threatened with discharge “because of his religiously compelled refusal to receive the vaccine.” 

The complaint said his request for a religious exemption was denied and his appeal rejected and he was told he’d be relieved of command by Feb. 14, 2022. 

The suit sought to prohibit the defendants from enforcing the vaccination policies against Dunn or “taking any adverse action against him based on his refusal to take the vaccine.” 

The case seeking a religious exemption ultimately went before the Supreme Court. According to his application for an injunction pending appeal, his attorney wrote that Dunn was removed from his command and he wanted “only protection against further punishment, including a discharge, because of his religious beliefs.” Ultimately, the application was denied by the court by a 6-3 vote in April 2022.

The case became moot while on appeal because Congress repealed the vaccine mandate, his attorney in the case, Donald Falk, said. 

The vaccine mandate was a contentious issue in the pandemic and forced more than 8,400 service members out of the military for refusing the shots and saw thousands seek religious and medical exemptions. The January decision by Defense Secretary Austin ended those exemption request.

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