The off-duty Alaska Airlines pilot who tried to shut off the engines on a Horizon Air flight from Everett told investigators he was “in crisis” after taking psychedelic mushrooms and not sleeping in almost two days, according to charges filed Oct. 24 in federal court.

Joseph David Emerson, 44, was charged in federal court in Oregon in connection with the midair incident on Horizon flight 2059, which took off about 5:25 p.m. Sunday from Seattle Paine Field International Airport bound for San Francisco.

After he was taken into custody, Emerson told Port of Portland police that he had consumed “magic mushrooms approximately 48 hours before the incident on the plane,” according to separate charges filed in Oregon courts by the Multnomah County District Attorney’s Office.

Emerson later told FBI investigators he believed he was having a “nervous breakdown,” that he had not slept in 40 hours, and that he felt dehydrated.

Due to the disturbance, the plane was diverted to Portland International Airport, landing there around 6:36 pm. Sunday. Emerson had been an Alaska Airlines employee for nine years and a pilot since 2001.

Emerson was traveling in the jump seat — a seat in the cockpit generally reserved for off-duty pilots and crew hopping between airports.

Crew members later told authorities that initially there was “zero indication of anything wrong,” with Emerson chatting casually on the flight deck about types of aircraft.

Then as the plane passed between Astoria and Portland, Emerson threw aside his headset and said: “I’m not OK,” according to federal charging papers.

“Yeah,” he reportedly later told investigators. “I pulled both emergency shut-off handles because I thought I was dreaming and I just wanna wake up.”

The emergency fire suppression system on the Embraer 175 consists of a red T-handle for each engine. If the T-handle is fully activated, a valve in the wing closes and shuts off fuel to the engine, according to an Alaska Airlines statement.

If he had succeeded in engaging the fire suppression system, it would have shut down the plane’s hydraulics and the fuel to the engines, turning the jet into a glider within seconds, according to the court documents filed by the FBI.

One of the two pilots operating the aircraft saw Emerson reach up and grab the red fire handles and begin to pull them down, according to the court documents.

The pilot grabbed Emerson’s wrist. Emerson initially resisted and they struggled for an estimated 25 to 30 seconds. The pilot’s actions prevented Emerson from pulling the handles all the way down, according to court papers.

In the meantime, the second pilot alerted air traffic control and declared an in-flight emergency, turning off the plane’s autopilot system and diverting the plane to Portland.

Emerson was physically restrained and escorted out of the cockpit. Emerson was reportedly handcuffed and a flight attendant led him to a seat in the back of the aircraft.

He allegedly told flight attendants: “You need to cuff me right now or it’s going to be bad.” During the flight’s descent into Portland, Emerson reportedly tried to grab the handle of the emergency exit.

Restrained in the back of the plane, Emerson allegedly told the flight attendants: “I messed up everything,” and that he had tried to “kill everybody,” according to the charges.

Radio traffic of the incident was recorded.

“We’ve got the guy that tried to shut the engines down out of the cockpit,” the Horizon crew can be heard telling air traffic control. “It doesn’t seem like he’s causing any issue at the back. I think he’s subdued. We want law enforcement as soon as we get on the ground and parked.”

Emerson acknowledged he tried to deploy the emergency handles that control the plane’s fire suppression system.

In custody, Emerson reportedly talked with a police officer about psychedelic mushrooms. Emerson said it was his “first time taking mushrooms,” according to the probable cause statement. The federal charges do not allege when exactly when Emerson consumed the mushrooms.

Interviewed by Port of Portland police, he allegedly said: “I’m admitting to what I did. I’m not fighting any charges you want to bring against me, guys.”

Emerson was initially arrested for investigation of 83 state counts of attempted murder, 83 counts of reckless endangerment and one count of endangering an aircraft. He pleaded not guilty to those charges Tuesday.

The federal charges list one more count: interference with flight crew members and attendants.

As of Tuesday, Emerson was being held at the Multnomah County Jail in Portland.

In a statement, Alaska Airlines officials praised the crew’s swift response.

“In this case, the quick reaction of our crew to reset the T-handles ensured engine power was not lost,” the airline wrote. “Our crew responded without hesitation to a difficult and highly unusual situation, and we are incredibly proud and grateful for their skillful actions. We are deeply proud of our Horizon flight crew and their quick actions both in the flight deck and in the rear of the aircraft.”

Passengers were able to complete their journey with a new crew and aircraft.

Emerson is a resident of Pleasant Hill, California, a Bay Area community 20 miles northeast of San Francisco. He received his most recent Airport Transport Pilot certificate in July. He is also listed as a certified flight instructor, according to the Federal Aviation Administration Pilot registry.

Emerson joined Alaska Air Group as a Horizon Air first officer in August 2001. In June 2012, Emerson left Horizon to join Virgin America as a pilot. Emerson became an Alaska Airlines first officer following Alaska’s acquisition of Virgin America in 2016. He became an Alaska Airlines captain in 2019. Throughout his career, Emerson completed his mandated FAA medical certifications in accordance with regulatory requirements, and at no point were his certifications denied, suspended or revoked.

Emerson has been removed from service indefinitely and relieved from all duties at Alaska Airlines, the Seattle-based carrier said in a statement.

This week, Alaska Airlines said it had reviewed the charging documents, “and, like many, are deeply disturbed by what we have learned.”