Off-duty Alaska Airlines pilot warned 'I am not okay' before alleged attempt to disable plane engines

"I am not okay," an off-duty Alaska Airlines pilot said before allegedly reaching and grabbing handles that could have disabled the aircraft's engines, according to a federal complaint filed on Tuesday.

Joseph David Emerson, 44, has been in custody since Sunday when a San Francisco-bound Horizon Air plane, which was operating Alaska Airlines Flight 2059, diverted to Portland International Airport after his alleged attempt to shut down the engines by engaging the fire suppression system, the airline said.

Emerson, based in Pleasant Hill, California, was charged in federal court with interfering with flight crew members, which carries a maximum penalty of 20 years in prison, the Justice Department said.

He was previously charged in Oregon with 83 counts of attempted murder, 83 counts of reckless endangerment and a count of endangering an aircraft, according to booking records from the Multnomah County Sheriff's Office.

Emerson was sitting in the jump seat of the aircraft and engaging in "casual conversation" with the plane's pilots at the beginning of the flight. Pilots regularly pick up jump seats in commercial cockpits to commute.

The pilots told investigators that there was no indication of anything wrong early in the flight, according to court records. But then, both pilots reported to investigators, Emerson shouted he was not OK and attempted to pull engine fire handles that would have cut off fuel to the engines.

One pilot said Emerson "had to be wrestled with" while the other pilot declared an inflight emergency and diverted to Portland, the court filing said. One of the flight's pilots told investigators that Emerson settled down after about 20 to 30 seconds and exited the cockpit.

After leaving the cockpit, Emerson told a flight attendant, "You need to cuff me right now or it's going to be bad." During the descent he tried to grab a handle of the emergency exit door, and was stopped by a cabin crew member, the document said. 

Emerson told investigators that he thought he was having a "nervous breakdown," hadn't slept in 40 hours, was dehydrated and tired, and that he became depressed about six months ago, the federal complaint said.

"I pulled both emergency shut off handles because I thought I was dreaming and I just wanna wake up," Emerson said according to the complaint, which cites police officers who interviewed him upon returning to the ground.

Emerson denied taking medication, according to the charging documents. He talked with an officer "about the use of psychedelic mushrooms" and "said it was his first-time taking mushrooms," the court filing said.

The DOJ didn't immediately return request for comment seeking clarity on when Emerson might have taken mushrooms.

"I'm admitting to what I did," Emerson said, according to the complaint, which added that he said he was waiving his right to an attorney. "I'm not fighting any charges you want to bring against me, guys."

Alaska said on Tuesday that Emerson had completed all his FAA-mandated medical exams and that his certifications weren't denied, suspended or revoked at any point.

The Seattle-based carrier said it reviewed the complaint and, "like many, are deeply disturbed by what we have learned."

Alaska said Emerson was approved to fly in the cockpit jump seat and that "at no time during the check-in or boarding process did our Gate Agents or flight crew observe any signs of impairment that would have led them to prevent Emerson from flying on Flight 2059."

The Justice Department affidavit is consistent with the airline's internal briefings with flight crew members, the carrier said, including that Emerson was placed in wrist restraints and strapped to a jump seat in the rear of the plane.

The carrier added that it and its Horizon Air subsidiary participate in the U.S. Transportation Department's drug testing program for on-duty crew members, which can include random testing as well as tests on suspicion of intoxication.

Alaska Airlines said it removed Emerson from service indefinitely, but that the airline is in contact with the Air Line Pilots Association, the pilots' union, about his employment status.

A lawyer for Emerson could not be immediately identified.

— CNBC's Gabrielle Fonrouge contributed to this article.