Call it “The Case of the Missing Conference Report.”

The episode may have begun as a mundane procedural matter, but in the space of a few hours on Thursday it swelled into a mystery that baffled staffers on both sides of the Capitol and left the future of a Federal Aviation Administration bill in doubt.

Innocently enough, the House of Representatives wanted to send the FAA reauthorization bill back to a joint House-Senate conference, bowing to union and Democratic demands to remove language in the conference report that would allow some air-traffic control towers to be privatized.

So at about 11 a.m. Thursday, staffers from the House Transportation and Infrastructure Committee politely called up the Senate Commerce, Science and Transportation and asked to have the original conference report documents sent back over to the House.

But, inexplicably, no one could find them. Had they been lost? Stolen? Intentionally hidden?

No one seemed to know, and that set off a three-and-a-half hour scramble of miscommunications, rifling through files, and House-Senate finger pointing.

“It was a bit of a caper,” acknowledged one Senate Commerce staffer.

When Senate Commerce aides couldn’t locate the papers initially, they told House Transportation aides to go looking for them on their side of the Capitol.

“We knew we didn’t have them, because we never had them,” explained Steve Hansen, Majority spokesman for the House Transportation panel. “But even though we knew we didn’t have them, we looked for them.”

Indeed, aides to Speaker Dennis Hastert (R-Ill.), who were anxiously waiting to bring the conference report back to the floor, were so convinced that Transportation had the paperwork that they demanded the staff look for them.

Even the House Parliamentarian believed the papers were in the possession of the House, according to aides.

Meanwhile, Senate Commerce aides were furiously searching for the papers as well. They finally called the Senate Parliamentarian’s office, which helped to produce a log book showing a Commerce Committee clerk had signed for the papers at the end of July, when the conference committee originally concluded its work.

Given that it had been nearly two months with no action on the FAA conference report, it seems the Commerce clerk didn’t initially realize or remember that the papers had been sent to the Senate panel. So when initially asked to produce them, the clerk said they weren’t there.

By 2:30 p.m. Thursday, the papers had been found where House Transportation aides had always believed them to be: in the Senate Commerce Committee. But House leaders had already decided around 1 p.m. to give up on trying to send the measure back to conference that day and adjourned early in the afternoon.

Now, it looks like the delay has given House Transportation Chairman Don Young (R-Alaska) an opportunity to have second thoughts about sending the bill back to conference to strip out the privatization language. He has decided not to move forward on changing the conference report until after a meeting with Senate Commerce Chairman John McCain (R-Ariz.) early next week, according to Hansen.

That’s raising some eyebrows, especially among those who already thought the lost paperwork was a ruse.

“I don’t think it got lost. I think it got stuck somewhere in Don Young’s office because he didn’t want it to go back” to conference, said one senior House GOP aide.

Another House Republican aide said it was probably the Senate, not the House, that was wary of going back to conference.

“A cynical person could say that they didn’t want [the House] to do that, and that’s why they ‘lost’ the paperwork,” the aide said.

And Democrats believe that Republicans in both chambers are reluctant to lose the fight over the air-traffic control towers and intentionally held up the measure to give Republican leaders more time to strategize.

“It’s easy to believe that there may be more to it than meets the eye, because of the way it’s been handled all along,” said Jim Berard, spokesman Rep. James Oberstar (D-Minn.), the House Transportation panel’s ranking member. “I can’t imagine why they waited until the 11th hour to go looking for these documents.”

Dave Matsuda, a spokesman for Sen. Frank Lautenberg (D-N.J.), noted that House leaders and Transportation panel staff knew the measure was coming to the House floor as early as Wednesday.

“They had the House markup for the Rules Committee the night before,” Matsuda said. “They had to have known about it ahead of time. Why didn’t they call the Commerce Committee then?”

Matsuda said the rumor in Senate Democratic circles is that McCain had a change of heart about sending the bill back to conference after it became clear a one-month extension of the FAA bill would be included in a continuing resolution, to keep the government running. Both chambers passed the CR with the FAA extension on Thursday.

With a month to work on it, perhaps McCain would try to figure out a way to bring the bill, unchanged, to the Senate floor, said Matsuda of the thinking among some Democrats.

McCain dismissed those rumors.

“To think we would resort to some sort of hiding papers — that’s just ridiculous,” McCain said.

Whether they send it back to conference committee or try another way to enact the bill, McCain and Young have a tough road ahead. Because the original impetus for including language to privatize as many as 69 small air traffic control towers came from a White House veto threat, the two are understandably nervous about giving in to Democratic demands.

But Democrats say all they want is to find a compromise between language that both chambers originally included in their FAA reauthorization bills that would explicitly prohibit the FAA from privatizing any new towers.

As for what really happened to the missing conference report, it’s anybody’s guess.

“I really don’t know the truth, and I don’t have any good speculation as to what happened,” noted Sen. Trent Lott (R-Miss.), who helped write the bill as chairman of the Commerce, Science and Transportation aviation subcommittee.