Last October, an off-duty pilot on an Alaska Airlines flight tried to crash the plane by shutting down the engines. That story is explored in “Lie to Fly,” and if it sounds like the kind of lurid true-crime rehash that’s usually fodder for a show like “Dateline,” that’s not the case.

“Lie to Fly” is the latest installment of FX’s “The New York Times Presents” documentary series and it is a moving and engrossing look at why this man suffered a psychotic break, but also why that’s connected to what many experts argue are counterproductive FAA rules surrounding mental health and the use of medications to treat anxiety and depression.

Joseph Emerson was a longtime pilot with the airline before that now- infamous flight. Married with kids, he has an unassuming appearance and he seems kind and reliable. But the sudden death of his best friend left him awash in grief. “It was the first time someone meaningful and significant currently in my life had just vanished.” Going to a psychiatrist who could prescribe antidepressants was a no-go. “I would immediately not be able to fly airplanes.”

That’s because the FAA has a lengthy procedure when it comes to medical certification for pilots who report health issues. “I can say with certainty that I have pilots who come to me and do not disclose medical conditions,” aviation medical examiner Brent Blue says. “I can say with certainty that pilots have come in who don’t disclose mental health issues. I think that’s actually a common issue, that lack of disclosure, because they do not want to go through the FAA process.”

The fear is that they will have their certification yanked for an extended period and won’t be able to work. That means some pilots are choosing to deal with issues on their own (in the words of the title, they lie to fly) and in Emerson’s case, that led to a terrible decision he clearly regrets.

While on a retreat in the mountains with friends, someone brought along psychedelic mushrooms and encouraged Emerson to give them a try. “People close to me that I trust are doing this substance and they say it makes them feel better.” He says it was out of character for him to even consider it, but at that point, with his depression untreated for so long, “my barriers to use had been taken away.” Instead of feeling a sense of calm or wonder, Emerson says he experienced paranoia — “very alone and very afraid, very fearful of these people that I know fairly well. I remember being afraid that they were going to kill me” — and says he was unable to tell whether he was dreaming or awake.

Two days later, when he arrived at the airport to catch a flight home, he was sleep-deprived and still extremely disoriented. Sitting in the jumpseat in the cockpit, he says his anxiety intensified and he reached for the controls before both pilots stopped him. Imagine having a nightmare and doing something rash to wake yourself up; that’s how Emerson describes the moment. When he was subdued and taken to the back of the plane, he told a flight attendant “I don’t know what’s real” and asked that she restrain him with cuffs. It was a devastating experience for all involved, and it was only when Emerson was back on the ground and arraigned in court that he finally understood “the enormity of what had just occurred. And that I was in real life.”

Emerson is out on bail and is still facing state and federal charges. His trial is expected to begin in the fall. Not mentioned here — and it’s a glaring omission — is why he and his attorney agreed to the interview. Is this an effort to influence perceptions around the case? Maybe. Neither of them comes across as cynical or manipulative and it was probably a smart choice to do the documentary because you feel genuine compassion for Emerson, who seems like a profoundly decent person in an awful situation and feeling deep shame about all of it. I suspect many will walk away thinking that if he’s found guilty, a prison sentence would be too harsh. Perhaps some viewers will feel less sympathy. But more transparency about the motivations behind Emerson’s participation in the project is warranted. As viewers, we should hold these kinds of journalism-branded endeavors to a high standard. That said, Emerson’s story is more of a case study for the documentary’s larger interests, which concern the FAA’s policies.

“Does a diagnosis necessarily mean a pilot is not fit to perform their duties? In many circumstances, that’s an open question,” says Dr. William Hoffman, a professor of aviation at the University of North Dakota. The experts interviewed here agree that there needs to be some common-sense improvements to how the FAA handles these issues.

A Chicago-area couple Alan Hauser and Anne Suh are interviewed about their son, John. He was a college student studying to become a commercial pilot. Three years ago, before taking off for a solo flight, he texted his parents to say he loved them. A few hours later, they learned that he had intentionally crashed his plane; here they speak thoughtfully and movingly about their story. In a note left by John, he writes: “If there’s anything you could do for me, get the FAA to change their rules on pilots seeking help for mental health.”

The documentary doesn’t say whether there are people who support the FAA’s current system, which would be good to know. But at least one representative of the agency makes clear that a lack of funding and staffing has created a backlog contributing to the long delays. The film also fails to examine standards for other professions. What are the rules around the use of antidepressants for locomotive engineers or bus drivers or truck drivers? Are those policies different from the FAA’s? If so, why? Again, if a project like this carries the imprimatur of a news outlet — if that is one of its main selling points — then it needs to be more journalistically rigorous.

Even so, “Lie to Fly” makes a persuasive case that the current system is failing everyone.

“A lot of pilots have mental health issues that they’re not disclosing,” Hauser says. “So we think the choice between healthy pilots and protecting the traveling public is a false choice. We think right now there are pilots in the cockpit who have mental health issues that are not being treated.

“So the real decision is, will the flying public be safer if we treat those pilots or if we don’t treat those pilots?”

How to watch: Hulu