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Then there is the question of deployments. Gen. Moseley would like to see the Raptor sent to wars in Afghanistan and Iraq. Positioning the radar-evading strike aircraft near Iran would send a powerful message to that country’s ruling mullahs. But so far, the plane, which went operational three years ago, has stayed out of combat. Its overseas deployments have been limited to an exercise in Japan. There are 40 combat-ready F-22s at the Langley, Va., Air Force Base.

“It’s very disturbing that the civilian people in the Pentagon are trying to minimize the extraordinary capabilities of the F-22,” said retired Lt. Gen. Thomas McInerney, who flew combat missions in Vietnam. “They want to cut the program. They want to stop it at 183.”

In another dispute, some of Mr. Gates’ staff want to create “joint” Air Forces bases in the Pacific operated by the Air Force and Navy. The Air Force opposes the plan.

And Mr. Gates stated publicly in April that the military was not doing enough to introduce futuristic unmanned aircraft. It was a clear shot at the Air Force, which wants to ensure there are always pilots in the air to control enemy airspace.

In return, the Air Force has openly challenged the defense secretary. Days after the White House requested a $117 billion Air Force budget for 2009, generals told the press it needed $20 billion more.

They said in February that the aging fleet of F-15 and F-16 fighters, which are to be replaced by the F-22 and F-35, average 20 years of age and far exceed the initial target of 4,000 flying hours.

Mr. Gates countered by privately rebuking an Air Force general, who simply stated in a press interview the service’s talking point: 381 F-22s.

“I think Moseley and Wynne would point out that the nation is not spending enough on defense,” Gen. Link said. “Defense as a whole has been gutted. My sense is they are convinced that we put the military on a war footing and did not put the nation on a war footing, and we are underfunding the military as a result, not just the Air Force.”

Gen. Moseley’s backers say that without these disputes, he might have survived the flap over lax control of nuclear weapons.

Mr. Gates says no. He told Air Force personnel, “There is no room for error in this mission; nor is there, unfortunately, any room for second chances, especially when serious questions about the safety and security of our nuclear arsenal have been raised in the minds of the American public and the international community.”

Some in the Air Force raised eyebrows over Mr. Gates’ choice to succeed Gen. Moseley. A bomber or fighter pilot has run the Air Force for decades. But the defense secretary picked Gen. Norton Schwartz, who flew cargo and special-operations aircraft.

Some in the Pentagon say the Air Force invites challenges inside the Pentagon by exhibiting an air of superiority. They still remember Gen. Merrill McPeak, then the chief of staff, holding a press briefing to explain how air power had essentially won Desert Storm in 1991.

And then there is the new Air Force recruiting slogan: “Above All.”

“The stupidest thing we did in a while was to adopt ‘Above All,’ which made us look like the biggest kids on the block,” said Gen. Link. “When the biggest kid on the block acts like he doesn’t care about the little kids, the little kids will find a way to bring him down.”