RIP Payne

On October 25, 1999, a month after the American team rallied to win the Ryder Cup and four months after his U.S. Open victory, Stewart was killed in the depressurization of a Learjet. He was flying from his home in Orlando, Florida, to Texas for the year-ending tournament, The Tour Championship, held at Champions Golf Club in Houston. Traveling on a Monday morning, Stewart was planning to stop off in Dallas to discuss building a new home-course for the SMU golf program.[29] The last communication received from the pilots was at 9:27 AM EDT, and the aircraft made a right turn at 9:30 AM EDT that was probably the result of human input.

At 9:33 AM EDT, the pilots did not respond to a call to change radio frequencies, and there was no further contact from the aircraft. The aircraft was apparently still on autopilot and angled off-course, as observed by several U.S. Air Force (and Air National Guard) F-16 fighter aircraft[30] as it continued its flight over the southern and midwestern United States. The military pilots observed frost or condensation on the windshield (consistent with loss of cabin pressure) which obscured the cockpit, and no motion was visible through the small patch of windshield that was clear.

National Transportation Safety Board investigators later concluded that the aircraft suffered a loss of cabin pressure and that all on board were incapacitated due to hypoxia as the aircraft passed to the west of Gainesville, Florida. A delay of only a few seconds in donning oxygen masks, coupled with cognitive and motor skill impairment, could have been enough to result in the pilots' incapacitation. The NTSB report showed that the aircraft had several instances of maintenance work related to cabin pressure in the months leading up to the accident. The NTSB was unable to determine whether they stemmed from a common problem. Replacements and repairs were documented, but not the pilot discrepancy reports that prompted them, or the frequency of such reports. The report gently chides Sunjet Aviation for the possibility that this would have made the problem harder to identify, track, and resolve, and the fact that in at least one instance, the aircraft was flown with an unauthorized maintenance deferral for cabin pressure problems.

According to a U.S. Air Force timeline, a series of military aircraft provided an emergency escort to the stricken Lear, beginning with an F-16 from Eglin Air Force Base, about an hour and twenty minutes (9:33 EDT to 9:52 CDT – see NTSB report on the crash) after ground controllers lost contact. The aircraft continued flying on autopilot until it ran out of fuel and crashed into a field near Mina, South Dakota, a town ten miles (16 km) west of Aberdeen, after an uncontrolled descent. The five other people aboard the aircraft included Stewart's agents Robert Fraley and Van Ardan, pilots Michael Kling and Stephanie Bellegarrigue, and Bruce Borland, a highly regarded golf course architect with the Jack Nicklaus design company.