In an Accident Investigation Board (AIB) report, the Air Force never found the original cause of the malfunction, but in a Statement of Opinion concluded "by clear and convincing evidence, the cause of the mishap was the MP's [mishap pilot's] failure to recognize and initiate a timely dive recovery due to channelized attention, breakdown of visual scan, and unrecognized spatial disorientation."
In an exclusive interview with ABC News in May 2012, Jennifer Haney said she immediately called the Air Force's conclusion into question and believed that, in addition to the original unknown malfunction's role, it seemed obvious her brother had blacked out while trying to save himself. Therefore, she said, he could not have been responsible for the crash.
"I don't agree with [the Air Force]. I think there was a lot more going on inside that cockpit," Jennifer said. "A cover-up? I don't know. But there's something... I'd like to think it's easier to blame Jeff. He's not here to defend himself."
Pierre Sprey, an early fighter jet designer and vocal critic of the F-22, said the Air Force's original report on Haney's crash was twisted to shield the aircraft from blame.
"From front to back, they're warping every fact you see in that thing, to make sure they will call it pilot error and not to blame [F-22 manufacturer] Lockheed [Martin] or not to blame the Air Force or the airplane," Sprey told ABC News in May. "Here you have a superb pilot and an airplane that wasn't designed to take care of him. And now they're blaming it on him and he shouldn't have died in the first place… The priorities are hardware first, people second."
In the course of its investigation, ABC News obtained an Air Force-made computer simulation of Haney's crash that shows that in the middle of Haney's oxygen-deprived dive, he doesn't appear to move the controls for approximately 15 seconds. Jennifer said that mysterious long pause in the middle of an emergency, along with the lack of a radio call, is evidence that her brother wasn't awake for at least part of the dive. Steve Ganyard, an ABC News consultant and former U.S. Marine Corps fighter pilot, said that after watching the computer simulation, he too believes Haney was unconscious at least part of the time.
"I think that [the Air Force's] conclusions are debatable at the very least... I just cannot believe that this pilot, as good as he is, knowing that the airplane is in an extreme position, is still conscious," Ganyard said.
Now, the Pentagon Inspector General's office says it agrees.
"It is unclear how sudden incapacitation or unconsciousness was determined to be a non-contributory factor by the AIB [Air Force Accident Investigation Board], or why levels of partial incapacitation or impairment were not considered," the IG report says.
Haney did appear to try to pull out of his dive three seconds before impact -- one second too late to save himself. The Air Force has said that was evidence he was not incapacitated and only disoriented before his death.
The question of Haney's consciousness is listed by the IG as one of five "deficiencies" in the AIB report, others including the uncertainty over the status of Haney's oxygen mask and his possible attempt to turn on an emergency oxygen system.
"The AIB report lacked detailed analysis of several areas," the IG report said.