Choice to Lead C.I.A. Faces a Changed Agency

Working closely with the president, Mr. Brennan oversaw the escalation of drone strikes in Pakistan in 2010 and was the principal architect of the administration’s secret counterterrorism operations in Yemen. He became a prominent public spokesman for the administration, appearing on television after foiled terrorist plots and giving speeches about the legality and morality of targeted killing.

The question that now faces Mr. Brennan, if he is confirmed by the Senate, is whether the C.I.A. should remain at the center of secret American paramilitary operations — most notably drone strikes — or rebuild its traditional espionage capabilities, which intelligence veterans say have atrophied during years of terrorist manhunts.

Four years ago, Mr. Brennan bowed out of consideration as Mr. Obama’s C.I.A. director in the face of claims from some human rights advocates that he had approved — or at least failed to stop — its use of brutal interrogation methods. He denied the accusations and ended up with a consolation prize, a job as the president’s counterterrorism adviser that most assumed would have offered a much lower profile.

By some measures, Mr. Brennan wielded as much power as if he had led the agency all along — an opportunity that was denied to him until now.

Some C.I.A. veterans and outside experts on Monday questioned whether Mr. Brennan, 57, who has been immersed in counterterrorism for years, is the right person to return the agency to its core mission of stealing secrets from foreign governments and providing long-term analysis.

“He’s going to have to think not just, ‘How do I hunt the latest terrorist?’ but ‘Where do I want this agency to be at the end of my term?' ” said Mark M. Lowenthal, a former senior C.I.A. official. Right now, he said, “everyone is playing Whac-A-Mole.”

Other current and former officials say that Mr. Brennan himself has worried that counterterrorism operations have consumed the C.I.A. and that he may welcome the chance to take a broader perspective.

“John often had to get involved in lots of tactical discussions, and this is a great opportunity for him to step back and view the agency’s mission strategically,” said Michael E. Leiter, who served as head of the National Counterterrorism Center in both the Bush and Obama administrations.

By sending Mr. Brennan to the C.I.A., Mr. Obama will be placing at the agency’s helm a man he trusts implicitly. But he is also sending an insider who spent 25 years at the agency and is unlikely to face the inbred skepticism and hostility that has sometimes greeted outsiders there.

Mr. Brennan spent most of his C.I.A. career as an analyst, but during the 1990s served a tour as the chief of the station in Saudi Arabia. From 1999 to early 2001, he was chief of staff toGeorge J. Tenet, the director of central intelligence, as the position was then called. At the end of his C.I.A. service, in 2004 and 2005, Mr. Brennan set up what is now the counterterrorism center.

Mr. Brennan’s nomination won swift praise from influential members of Congress. Both Senator Dianne Feinstein, Democrat of California and chairwoman of the Senate Intelligence Committee, and Representative Mike Rogers, Republican of Michigan, her counterpart in the House, issued statements of support. Mr. Rogers congratulated Mr. Brennan and added, “I look forward to working with him.”

But Senator John McCain, Republican of Arizona, who was tortured as a prisoner of war in North Vietnam and has taken a strong stand against coercive interrogations, expressed reservations. “I have many questions and concerns about his nomination,” Mr. McCain said in a statement. He said he was especially concerned about what role Mr. Brennan “played in the so-called enhanced interrogation programs while serving at the C.I.A. during the last administration, as well as his public defense of those programs.”