Pilot Michael Johnston dies during American Airlines flight

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(CNN)Medical emergencies are rare, but hardly unprecedented in commercial flights.

It’s far less common when they involve the plane’s pilot — and that pilot dies.

That’s what happened Monday on an American Airlines flight between Phoenix and Boston.

Captain Michael Johnston, 57, was piloting the plane when he fell ill somewhere en route. The co-pilot landed the jet safely.

Crew members “took extraordinary care of Mike, each other and our customers,” airline CEO Doug Parker said in a statement sent to employees.

“We couldn’t be more proud of the teamwork this crew showed during an extremely difficult time.”

American Airlines pilot dies mid-flight, co-pilot lands

American Airlines pilot dies mid-flight, co-pilot lands 02:17
An autopsy and preliminary toxicology tests “showed that the death was the result of natural diseases,” the Onondaga County, New York, medical examiner’s office said — without offering specifics.

Johnston’s wife told CNN affiliate KUTV had a double bypass surgery in 2006. She said she was told he likely died of a heart attack.

“Whatever happened in the cockpit, none of us will know,” passenger Frank Cacciola told CNN affiliate WCVB.

Cacciola was among the 147 passengers and five crew members aboard Flight 550 when it took off around midnight, heading from the Southwest to the Northeast. Their Airbus A320 plane was being operated by U.S. Airways, which is now part of American.

The pilot fell ill somewhere en route, and the flight was diverted to Syracuse in upstate New York.

“Medical emergency, captain is incapacitated,” someone in the cockpit told an air traffic controller, according to audio posted to LiveATC.net. “Request handling for runway.”

Those on board knew something was wrong when a woman’s “quivering” voice came over the intercom, alerting them the pilot was sick, passenger Peter McSwiggin told WCVB.

According to passenger Julia House, passengers waited for the body to be removed. They made it to Boston after noon, nearly five hours after their scheduled time.

Passengers expressed sadness about what happened and gratitude they arrived safely.

“If it wasn’t for the copilot using a cool head,” McSwiggin said, “it might have been more disastrous.”

CNN’s Tina Burnside, Joseph Netto and Kristina Sgueglia contributed to this report.

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