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The Bureau of Alcohol, Tobacco, Firearms and Explosives has been taking a beating. Republicans in Congress issued a scathing report this week. It concludes that management failures set the stage for the recent Fast and Furious scandal. ATF agents involved in the operation lost track of weapons later found at crime scenes along the Southwest border.

Earlier today, the man brought in to turn the agency around sat down for a rare interview with NPR's Carrie Johnson.

(LAUGHTER)

B. TODD JONES: Yes, we are under the microscope, so to speak.

CARRIE JOHNSON, BYLINE: Here's the first thing you need to know about Todd Jones, the acting director of the Bureau of Alcohol, Tobacco, Firearms and Explosives: He's a former U.S. Marine. And when Justice Department officials asked him to help fix the ATF, Jones answered the call to duty.

JONES: August 30th of 2011.

JOHNSON: A memorable day.

JONES: A very memorable day. It was the first time I'd ever walked into ATF headquarters, and it's been a sprint for the last year.

JOHNSON: A sprint to change policies that might have led to the Fast and Furious scandal. Jones put in place new monthly oversight for big investigations, cases where dozens of firearms appear to have been purchased illegally. He also laid down new limits on how ATF agents operate undercover and how they deal with confidential informants.

Jones has replaced six out of his eight top assistants at Washington headquarters. And he says he's tried to promote a new generation of leaders all over the country, including ground zero for the scandal, along the Southwest border.

JONES: Sixteen out of our 25 field divisions have new special agent in charge. It's really a historic transformation. And it's really been an opportunity for us to cherry-pick our best and brightest.

JOHNSON: But five ATF managers in Washington and Arizona who were blasted by House Republicans in their report on Fast and Furious still work in the federal government, a point that seems to rankle Fox News host Megyn Kelly and California Republican Congressman Darrell Issa.

MEGYN KELLY: Of these five guys who you point to, who are responsible for this at ATF, no one has been fired. They're still on the federal taxpayer dime. And the head guy, Ken Melson, he's working for DOJ right now. Are the taxpayers still paying all these folks and why?

REPRESENTATIVE DARRELL ISSA: They are still paying all these folks. We are concerned that there has been no real repercussions.

JONES: On this issue of folks who are identified in the House report that are still with ATF...

JOHNSON: Todd Jones.

JONES: Well, there's this little concept called due process. And until we get a factual report and a complete record from the Department of Justice's Office of Inspector General, then there are rights that employees have.

JOHNSON: That inspector general report could come out within weeks, beginning a new chapter for the ATF. Like other parts of the federal bureaucracy, the budget's flat. There's a hiring freeze. And there's another complication, the politics of gun ownership.

JONES: The things that we do are limited by the state of the law, and there is a legal commerce in firearms in the United States.

JOHNSON: Jones resists calling for new legislation. He says he's not sure if or when the agency will have a leader who's confirmed by the Senate. That hasn't happened for the past decade, through both Republican and Democratic administrations. Instead, Jones says, he's focused on what he can change, sending agents surging into places where violent crime has ticked up: Oakland, New Orleans, Philadelphia.

For the past year, Jones has been commuting between Washington and his home in Minnesota, where he's the top federal prosecutor. Lots of packing and unpacking his old military sea bag.

JONES: My wife and I learned how to do the sea bag drag and, you know, spend time apart and still have things operate smoothly. So she's great, and we're used to living out of a suitcase or a sea bag.

JOHNSON: Ever the military man, Jones says he'll stay at ATF as long as his bosses at Justice need him.

Carrie Johnson, NPR News, Washington.

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