James Clapper, the director of national intelligence (DNI), is not your sleek, button-down spy chief. The 72-year-old retired Air Force general has a beatnik goatee, a tendency to speak in malapropisms and a cranky attitude that he sometimes sums up with the phrase “I’m too old for this [expletive]!”

The structure of Clapper’s position overseeing the nation’s 16 intelligence agencies has itself been a kind of bureaucratic nightmare. The post was created in 2004 to reduce the turf wars within the intelligence community that had prevented “connecting the dots” before Sept. 11, 2001. But although the legislation promised to empower a real intelligence chief, it kept key budget and management powers within the Pentagon — with the result that the DNI initially added more layering and second-guessing than efficiency.

The log-rolling and infighting that produced the unwieldy DNI structure is explained in a fascinating new book, “Blinking Red,” by Michael Allen, former staff director of the House intelligence committee and now with Beacon Global Strategies. He quotes former CIA director George Tenet describing the law as “a mad rush to rearrange wiring diagrams in an attempt to be seen as doing something.” Bob Gates, the White House’s first choice for DNI, refused because he thought it was “doomed to fail.” Clapper himself warned that a “feckless” DNI would make things worse.

But there are welcome signs that this jury-rigged structure may finally be starting to work as the DNI responds to budget pressures and the scandals surrounding National Security Agency’s surveillance programs. Clapper has recently taken steps that forced the National Security Agency (NSA) to accept greater transparency and stopped the military agencies from wasteful spending on duplicative satellite imagery.

Clapper is using management powers that were muddled under the confusing 2004 law. Rather than look over the shoulders of his 16 client agencies, as previous DNIs tended to do, Clapper has instead pushed more collaboration — something that’s easy to talk about but hard to do in an intelligence culture that rewards protection of secrets. The intelligence community is still way too big and turf-conscious, and it combines the worst features of bureaucracy and secrecy. But at least someone is trying to manage this secret empire.

One example is Clapper’s pressure on the NSA to disclose more about its surveillance programs. The NSA initially wanted to “redact” (a fancy word for censor) far more of a 2011 ruling by the Foreign Intelligence Surveillance Court that the agency had engaged in illegally broad surveillance. Clapper thought NSA lawyers were suppressing too much, so he instructed his general counsel, Robert Litt, to go back through the document and make public more information. Clapper ignored NSA and Justice Department protests, including to the White House, and backed Litt’s less-redacted version.

Another example involved the intelligence community’s purchase of commercial overhead imagery. The United States was paying two companies, GeoEye and Digital Globe, for duplicative coverage. Clapper backed a Pentagon effort to end the GeoEye contract, saving the government millions. Clapper has also tried to streamline the wildly expensive classified spy-satellite programs, trying (not always successfully) to avoid attempting too much with each satellite.

Clapper also used his budget authority to reduce the impact of sequestration. He refused to furlough most people involved in the so-called national intelligence program, and (unsuccessfully) pushed the Pentagon not to furlough its employees involved in the military intelligence program.

The White House has generally deferred to Clapper, letting him broker deals within the intelligence community rather than try to impose its own management. On redaction of NSA documents, for example, the White House left most decisions with Clapper.

Rep. Mike Rogers, the Michigan Republican who chairs the House intelligence committee, says he thinks the DNI structure under Clapper is “vastly improved” from where it was a few years ago, including “much better” fusion of intelligence in the president’s daily brief.

Rogers said he also supports Clapper’s efforts to disclose more information about NSA programs where that’s possible without damaging security. “We’ve got to have some confidence-builders and show the public that these programs are as transparent as they can get while still being effective.”

Back when the DNI legislation was being drafted, Clapper argued at a 2004 lunch with Donald Rumsfeld, then secretary of defense, that the country needed a strong position that would be the equivalent of secretary of intelligence. Allen writes that Rumsfeld “slammed his fork into his plate” and said it would be a “terrible idea.” By seeking consensus rather than issuing directives, Clapper is beginning to figure out a way to make the fuzzy DNI structure work after all.

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