The first operational F-22A Raptor is flown to its permanent home at Langley Air Force Base, Va., on May 12, 2005.

The Air Force has spent tens of millions of dollars over the past two years correcting problems with its premier jet fighter -- issues that Capt. Joshua Wilson helped expose by speaking up, both to his bosses and on national television.

Since then, Wilson's career as an F-22 Raptor pilot has stalled. A member of the Virginia Air National Guard's 149th Fighter Squadron, Wilson hasn't been permitted to fly the jet since early 2012. He's fighting disciplinary actions that he sees as retribution for going public.

"I'm a fighter pilot. I worked my entire life to get in the cockpit and to that job," said Wilson, who is 37. "Right now, I'm fighting the Air Force when I should be fighting our enemies."

Almost two years ago, Wilson and Maj. Jeremy Gordon told CBS's "60 Minutes" that the F-22 had a defective oxygen system that was endangering pilots.

The veteran aviators, dressed in their Virginia Air National Guard flight suits, shared their personal accounts of mid-flight oxygen deprivation that left them disoriented. Other pilots had similar life-threatening experiences but were reluctant to speak publicly, they said.

The Pentagon's top brass took notice.

Then-Defense Secretary Leon Panetta demanded that Air Force leaders accelerate their efforts to fix the problem. He asked NASA and the Navy to help, and he restricted Raptor flights so pilots experiencing problems would be close to a landing field. Members of Congress weighed in, too.

Back at Langley Air Force Base, Virginia Air National Guard leaders were also taking action. Even before the "60 Minutes" segment aired in May 2012, the squadron's leadership began a series of punitive measures against Wilson.

In April 2012, they stopped his planned promotion to major, and they threatened to take away his wings, jeopardizing his military career.

They also forced him out of his full-time desk job with the Air Force's Air Combat Command at Langley.

During that time, Wilson alerted the Department of Defense's office of inspector general, which is investigating. He and his lawyers say the Virginia Air National Guard's actions are reprisal for speaking out.

Cotton Puryear, a Virginia National Guard spokesman, declined to discuss the actions against Wilson. Guard leaders are waiting for the inspector general's probe to be completed before they "take appropriate action to resolve any outstanding issues," Puryear wrote in an email.

No such disciplinary problems haunt Maj. Jeremy Gordon, who sat next to Wilson in the interview with "60 Minutes" correspondent Lesley Stahl.

Gordon, a decorated pilot who flew an F-16 in the Iraq War, voluntarily stopped flying the Raptor in mid-2012. He remains a part of the squadron, flying a T-38 trainer jet.

"There are not and never were any personnel actions initiated regarding Maj. Gordon," Puryear wrote.

Wilson said he has refused overtures from his leaders to walk away. He wants a chance to clear his reputation and get back in the cockpit.

"If you guys can prove I'm a bad officer, kick me out of the military," he said. "If not, let me get back to my job. Let me get back to what I love to do, what I'm good at and what I trained my entire life to do."

U.S. Rep. Adam Kinzinger, an Illinois Republican and Air National Guard pilot, said he believes Wilson is being punished both for speaking out and for aggressively pushing, internally, to solve equipment problems.

"I have no doubt that this is reprisal," said Kinzinger, who attended officer training with Wilson a dozen years ago and helped arrange the "60 Minutes" interview. "There's no excuse for what's happened.... I think they basically believe they could outlast Josh."

U.S. Sen. Mark Warner of Virginia has also pressed the Air Force to fix the plane and is critical of how Wilson has been treated.

Warner said Wilson's treatment doesn't necessarily constitute reprisal.

"But I am going to say something doesn't smell right when the Air Force has had to acknowledge there's a problem and takes a fix. And somebody is still hanging out two years later with his career in jeopardy," Warner said.

The F-22, which entered active service in 2007, was plagued with problems with its oxygen system. Pilots reported hypoxia-like symptoms, including becoming disoriented, nauseous and extremely fatigued. In November 2010, an Alaska-based Raptor crashed, killing the pilot, after the plane's oxygen system malfunctioned.

Wilson's firsthand experience came on Feb. 16, 2011, when he became so disoriented while flying off the Virginia coast that he was unaware his hand movement on the controls was causing his plane to rock. He had unknowingly changed his radio frequency so that ground control couldn't reach him, and he couldn't read his own writing. Sensing he was having a problem, he tried to find the emergency oxygen supply ring he knew was on the left side of his seat. But in his bewildered state, he couldn't find it.

When he finally engaged the backup air supply, Wilson's head cleared, and he landed at Langley. Afterward, he suffered severe headaches, vertigo and bouts of exhaustion. It was only after three stints in a hyperbaric chamber -- used to treat oxygen deprivation -- that Wilson felt he had recovered.

A few months later, the Air Force grounded the entire Raptor fleet.

When the F-22 was cleared to fly again in September 2011, the Air Force had added a charcoal filter to the breathing system in the hopes of trapping contaminants. But that fix appears to have presented new problems.

In the months that followed, pilots discovered the filters were releasing charcoal dust inside their oxygen hoses. The result, according to a letter Wilson's lawyer sent to the inspector general: coughing fits and other respiratory ailments.

Members of the squadron, including Wilson, told their commander they wanted to fly without the filter but were informed that anyone who refused would face disciplinary action.

After about 40 hours of flying with the filter, Wilson developed an "uncontrollable cough, dry, scratchy, sore throat and the inability to take a deep breath," he said in a memo sent to Col. David Nardi, then commander of the 192nd Operations Group.

Feeling that not all pilots were reporting problems with the Raptor, a small group of officers at Langley -- including Wilson and medical personnel -- developed a confidential survey for F-22 pilots. They wanted to learn more details about symptoms of oxygen deprivation from aviators, who are generally reluctant to discuss health problems that might ground them. Before it could be administered, the 106-question survey was rejected by Virginia Air National Guard and Air Force leaders.

Wilson didn't stop asking questions, though. He sent several emails to senior Guard officers asking specifically about the charcoal filter and other health monitoring equipment that Raptor pilots had begun to wear.

He acknowledged both those activities irritated his commanders, but his resistance to flying with the charcoal filter appears to be the central issue in the disciplinary action against him.

In the early months of 2012, pressure from his superiors to fly using the filter grew more intense. They would demand he fly with the filter; he would respond by saying that an Air Force flight doctor and a pulmonologist advised him that doing so would damage his lungs.

Things came to a head in April 2012. Wilson described the chain of events in a complaint letter to the inspector general:

In an April 5 meeting, Col. Howard Purcell, the vice wing commander, pressed him to fly with the filter and told him his expected promotion to major -- in the works for several months -- had been suspended.

That evening, Nardi called Wilson to tell him that he was no longer permitted to work at Air Combat Command, where he was involved in planning air security during the 2012 presidential election. As a Guard pilot, he needed Nardi's permission for the desk job, which paid $60,000 a year -- most of his income.

A little more than two weeks later, Nardi gave Wilson a letter of reprimand for failing to fly the F-22.

The April 21 letter made no mention of Wilson's explanation that his military doctors told him not to fly with the filter. Nardi also wrote that Wilson needed to "immediately rectify" his combat-ready status by flying the F-22 or he would "face far more severe consequences, to include the untimely end of your military career."

If the reprimand was meant to provoke Wilson to get back in the cockpit, he wasn't given much time to comply. The next day, the Virginia Air National Guard blocked him from flying.

On April 22, he was given a second letter, this one signed by Col. Thomas Wark, Nardi's boss, stating that a flying evaluation board would convene to consider whether to take away Wilson's wings -- and his livelihood. His aviation privileges were suspended immediately.

"Your apparent fear of flying the F-22 is evidence of a habit, trait of character or personality characteristic that makes it undesirable for the command to continue using you in flying duties," Wark wrote.

The correspondence noted Wilson had been reprimanded a day earlier and said his failure to fly "constitutes a conscious decision" not to meet training requirements. It did not mention that military physicians had told Wilson that he should not fly with the filter.

Wilson insisted he never refused to fly the F-22; he asked for a waiver to fly without the filter and was denied.

Even as Wilson was being pressed to fly with the charcoal filter, senior Air Force leaders had decided to stop using it. The canisters were removed in April 2012 partly because they were making it more difficult for pilots to breathe -- exacerbating the problem they were attempting to solve.

Wilson's annual performance evaluations have suffered since speaking out.

Four years of reviews by his superiors at Langley and in New Jersey, where he flew the F-16, were filled with praise and talked of his promise as an officer.

In February 2012, the Virginia Guard leadership called him a "premier tactician" who was making "outstanding progress" in flight lead upgrade training that would prepare him for a leadership role. His commander wrote that Wilson was "one of my top wingmen" and a "superb officer, aviator and volunteer."

But the tone turned sharply critical -- bordering on sarcastic -- in a review written after he went public about the F-22.

It described Wilson as an "average officer" during 2012. Without mentioning his television appearance, the review, which Nardi approved, described Wilson as a "photogenic, driven and vocal officer; willing to express and share views regarding F-22A operations at all levels."

Maj. Gordon, who appeared on "60 Minutes" with Wilson, declined to be interviewed for this report.

Given Gordon's war record and aviation experience, his decision to stop flying the F-22 apparently troubled Gen. Mark Welsh III, the Air Force chief of staff. The four-star general, who, like Gordon, began his career as an F-16 pilot, telephoned Gordon last year to ask whether he wanted to fly the F-22 again, according to a source familiar with the conversation. Gordon declined.

The Air Force says it has significantly addressed the Raptor's oxygen system problems, and it notes there haven't been any unexplained physiological incidents in more than two years. It is installing a new backup emergency oxygen system in the Raptor that starts automatically when sensing a pilot is having trouble. As of last week, the system has been installed in 20 of Langley's 46 Raptors. All are expected to be upgraded by September.

Wilson said he is glad that the plane is being fixed but is frustrated his career remains in limbo. The inspector general's office, which has visited Langley for interviews, hasn't indicated when it will conclude its investigation.

Despite the controversy, Wilson said, he's never lost his love of the F-22.

"It's a huge honor to fly this airplane.... It's an unbelievable machine," he said.

He doesn't regret his activism.

"Somebody's got to take a stand," Wilson said. "It's no doubt that if we had continued on the path we were on, we would've had another accident.... We were waiting for it to happen."

bill.bartel@pilotonline.com