In late October, the man ostensibly in charge of America's 16 intelligence agencies decided to push out his most powerful subordinate. James Clapper, the director of national intelligence, had learned that CIA Director David Petraeus had an affair with his biographer – one that had attracted the scrutiny of the FBI. Clapper urged Petraeus to resign. That set off a chain of events leading to President Obama nominating his main counterterrorism and intelligence adviser, John Brennan, to replace Petraeus.

Never before has a Director of National Intelligence actually exercised that kind of power; the DNI's role has been a bit murky ever since the job was created in 2004. But the firing of Petraeus might also have been something of a high-water mark for the DNI. "Clapper can't do to Brennan what he did to Petraeus," says one former intel officer.

If confirmed by the Senate to lead the CIA, John Brennan, to paraphrase Daniel Day-Lewis in Lincoln, will be clothed in immense power. He's already an architect of the CIA's accelerated counterterrorism campaign, the one that launches drone strikes at suspected terrorists around the world. From his perch at the White House, Brennan has been a major advocate for the CIA, perhaps more effectively than the men running Langley, thanks to his close relationship with Obama.

Intelligence veterans expect all that to remain when Brennan goes to the CIA – with one major difference. "Now he's got a huge agency at his disposal," says Amy B. Zegart, an intelligence expert at Stamford University. "James Clapper just lost of a lot of power."

Intelligence veterans who've worked with Brennan don't expect him to make major changes at Langley. After all, much of the CIA's focus during the Obama administration has come under Brennan's somewhat removed watch. Those who want to see the CIA hand over control of the drone program to the U.S. military – a position that the Washington Post reported Brennan was sympathetic to in the White House – may be disappointed.

"It may be that once he's sitting at CIA and has his hand on the joystick, as it were, he may be reluctant to divest control to the military," says Robert Grenier, a former director of the CIA's Counterterrorism Center. "There's little question that both for substantive and political reasons the war on terrorism is still on the front burner, and he's certainly not going to take his foot off the gas with regard to the war on terrorism."

Which is likely what Obama wants. By putting Brennan at the CIA and former Senator Chuck Hagel at the Pentagon, Obama's national security predilections come into focus: aggressive but secretive wars with minimal troop and logistics footprints, matched with winding down the long slog in Afghanistan.

But that's not to say the drone war will remain exactly as it is. As the Council on Foreign Relations' Micah Zenko notes in a report to be released tomorrow, the secretive drone campaign has often been at odds with America's publicly-stated foreign policy. (Full disclosure: Noah Shachtman served on the advisory board for the report.) Last February, Secretary of State Hillary Clinton told the International Contact Group on Somalia that "airstrikes would not be a good idea. And we have absolutely no reason to believe anyone—certainly not the United States—is considering that." Within hours, an American drone strike in Somalia killed at least four people. In September, the President insisted that the drones are only striking extremists who are plotting to attack the U.S. or its interests; yet there have been dozens of "signature strikes" in which the drones unleash their weapons just because the targets appear to look and act like terrorists. Zenko is pushing for an end to the signature strikes – or a major, public explanation of how they "meet the principles of distinction and proportionality that the Obama administration claims."

Either way, Brennan suddenly looks like the most powerful member of Obama's national security team. Hagel looks like he may face a tough confirmation fight, and in any event is new to the Pentagon, a management challenge like no other. Other top members of the national security apparatus, like Secretary of State Hillary Rodham Clinton, are leaving also. White House sources say it's yet to be determined if anyone on the National Security Council will retain Brennan's enlarged portfolio over intelligence, counterterrorism and homeland security efforts.

"Brennan is The Guy now," Zegart notes. "There's no more important asset, coming into the head of the agency, than having that kind of trust of the president. Brennan is possibly unique in that respect: I can't remember an incoming CIA director with that kind of relationship with the president."

Not everyone at the CIA is thrilled by the Brennan pick. The Arabic-speaking Brennan has held a variety of CIA jobs, with an unusual upward career trajectory. He went from being an intelligence analyst to serving as CIA station chief in Saudi Arabia – a job ordinarily reserved for someone from the agency's cloak-and-dagger types in the Directorate of Operations. Later, Brennan worked as chief of staff for CIA Director George Tenet. His abrasiveness occasionally irritated his thin-skinned colleagues, and he engendered no small share of professional jealousy along the way.

Playing the bad cop role is traditional for a chief of staff, of course. But Brennan slid into so naturally, he reminded one former intelligence officer in retrospect of a famously crusty #2 from science fiction.

"Remember Col. Tigh from Battlestar Galactica? That's who Brennan was. He rubbed a lot of people the wrong way," the officer says. "He's a tough, hard-nosed bastard. He scared the shit out of people. I really liked him."

To some degree, Brennan's power comes at the expense of one of the national security officials who remains in place: Clapper. Like his predecessors, Clapper holds an uncertain bureaucratic hand: the director of national intelligence has poorly-defined legal authority over the various intelligence agencies and the $75 billion annual intelligence budget. Those authorities have also been weakened over time by turf battles: Clapper's predecessor, Dennis Blair, resigned in 2010 after losing a struggle with then-CIA chief Leon Panetta over the right to appoint CIA station chiefs overseas. Clapper also reached his perch thanks to his ties to Defense Secretary Robert Gates, but Gates left the Pentagon in 2011.

For his part, Clapper cheered Brennan's appointment, calling Brennan a "strong leader" in a statement to the press. But putting one of Obama's closest advisers in a theoretically subordinate position to Clapper puts the ostensible head of the intelligence community in a bind. One agency veteran, when asked about the future role for the director of national intelligence, laughed for twenty seconds straight.

Of course, any tenure at the CIA is bound to have complications; Brennan's will be no exception, if he's confirmed. The CIA's former directors are openly warning that the agency has to widen its focus beyond counterterrorism and return to its roots of traditional spycraft. One indication of that shift, agency veterans believe, will be whether Brennan keeps John Bennett, the current head of the undercover spies of the National Clandestine Service. On Capitol Hill, the chairwoman of the Senate intelligence committee, Dianne Feinstein (D-Calif.), lent her support to Brennan on Monday, but Sen. John Cornyn (R-Tex.) is threatening to block his nomination until the White House discloses more about national security leaks.

"If the president wants the CIA involved in it – for variety of reasons, keeping it lower key, secret – then they'll do that," says Tyler Drumheller, a former CIA operations chief in Europe. "If he wants to say is it's the province of the military, [Brennan] will do that. ... If that's what the president wants, it's what John will do."