• The off-duty pilot was traveling in the cockpit of a Horizon Air plane, a regional carrier owned by Alaska Airlines.
• Joseph David Emerson, 44, has been in custody since Sunday.
• One pilot said Emerson "had to be wrestled with" while the other pilot declared an inflight emergency and diverted to Portland, Oregon, the court filing said.

"I am not okay," an off-duty Alaska Airlines pilot traveling in a cockpit jump seat said before allegedly 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.

State and federal court documents filed Tuesday described a brief struggle between Emerson and one of the flight's pilots before Emerson was restrained at the back of the plane. Emerson told investigators that he had been depressed, not sleeping and had taken psychedelic mushrooms about two days before the incident, the documents 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. He pleaded not guilty to those charges on Tuesday, the Associated Press reported.

'Casual conversation'

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. 

'I thought I was dreaming'

Emerson told investigators that he thought he was having a "nervous breakdown," was dehydrated and tired, 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 federal court filing said.

A spokesman for the local Justice Department's office declined to comment further.

Emerson told a police officer and medical personnel that he took "magic mushrooms" 48 hours before the incident on the plane, according to a separate set of state court documents. Those documents said Emerson told police that a friend of his recently passed away.

No signs of intoxication

"I'm admitting to what I did," Emerson said, according to the federal 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 that 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.

State court documents listed attorney Noah Horst as representing Emerson in state court Tuesday. A lawyer in the Portland area with that name didn't immediately return request for comment.

— CNBC's Gabrielle Fonrouge contributed to this article.