A multilingual CIA veteran from New Jersey who shares the president's love for basketball, Mr. Brennan is Mr. Obama's envoy to what former Vice President Dick Cheney called the "dark side": the community of analysts, operators and intelligence managers who work with allied security services to disrupt terror networks.
The job — officially known as homeland security adviser and deputy national security adviser for counterterrorism — is in part a consolation prize for being passed over as director of the CIA.
As the CIA's deputy for management, Mr. Brennan played no role in developing the interrogation program that included the waterboarding of three suspected al Qaeda leaders, said John McLaughlin, CIA deputy director at the time.
"His duties at the time did not include that issue," Mr. McLaughlin told The Washington Times.
Still, the incoming Obama administration's sensitivity about the torture subject appears to have led to the decision to give Mr. Brennan a job that requires no Senate confirmation.
Given a complicated bureaucratic structure in which a director of national intelligence now outranks the CIA director, Mr. Brennan may wind up being more influential inside the White House than outside.
Denis McDonough, deputy national security adviser for strategic communication, said Mr. Obama meets with Mr. Brennan before any major intelligence briefing.
"The fact is the president seeks John's views and reactions to every terrorism and homeland security issue," Mr. McDonough told The Times. "There is no question about that."
A native of North Bergen, N.J., Mr. Brennan grew up in a multiethnic neighborhood that prepared him for encountering different cultures abroad.
Former FBI Director Louis Freeh, who grew up a few blocks from Mr. Brennan and whose father sold the Brennans their home, said, "No matter where we were in the world, we could always pronounce people's names because all these guys were in our public school classes."
Even though they share a hometown, the two did not meet until the late 1990s when Mr. Brennan served as the CIA station chief in Riyadh, Saudi Arabia. At the time, Mr. Freeh was investigating the 1996 bombing of a U.S. Air Force housing facility known as Khobar Towers.
Mr. Freeh said he would at times have to wait until 3 or 4 in the morning for meetings with high-ranking Saudis and in each of these cases, Mr. Brennan would wait with him.
"He had a good sense of humor," Mr. Freeh said. "The agents we posted there, they had a lot of respect for him. They would also tell you he was a good guy." Mr. Freeh noted that it is high praise for an FBI agent about someone in the CIA.
Mr. Brennan, a fluent Arabic speaker, first visited the Middle East in 1975, spending two semesters at the American University in Cairo.
Charles Kestenbaum, who at the time was an NBC reporter, said Mr. Brennan played power forward and center on the university's basketball team, often dominating the shorter Egyptians.
"It was a wonderful time to be Americans in Cairo. We were not political, we were enjoying the benefit of the good relations at the time," Mr. Kestenbaum said. Egyptian President Anwar "Sadat had just started opening up the country. Everywhere we went, people were friendly and welcome. John was a pretty big guy. He stood out, but he went everywhere he could."
Four years later, Mr. Brennan joined the CIA's clandestine service. He is among the few CIA officers to have both served in the field and as an analyst at headquarters.
Former colleagues hold him in high regard. Mr. Brennan is "someone you go to to get a second opinion on something you are struggling to decide," Mr. McLaughlin said. He said Mr. Brennan also stressed the al Qaeda threat in the summer before Sept. 11.
In the aftermath of the attacks, President Bush assigned Mr. Brennan to set up a clearinghouse of analysts and operators to monitor terrorist threats and lead tactical missions to disrupt them. Originally called the Terrorist Threat Integration Center, the unit is now the National Counterterrorism Center (NCTC) — a post-Sept. 11 innovation that Mr. Obama intends to build on, according to White House officials.
Fran Townsend, one of Mr. Brennan's predecessors as White House adviser on counterterrorism and homeland security from 2004 to 2008, compared the NCTC to the counterterrorism unit in the Fox television drama "24." She said Mr. Brennan was a little bit like that show's protagonist, Jack Bauer, in terms of focus, professionalism and seriousness.
Ms. Townsend recalled Mr. Brennan's poise during a crisis in 2004 when there was credible information about a terrorist plot targeting the New York financial district and World Bank headquarters in Washington.
Participating via secure video-teleconferencing, Mr. Brennan would kick off the meetings. "He was unflappable, his advice was clear and direct," Ms. Townsend said. "I would rely on his advice on the credibility of the threat and what more we needed to do."
Mr. Brennan declined a request for an interview.
However, he told The Times' Bill Gertz in October during the presidential campaign that counterterrorism went beyond military activities and attempts to "divide the world between good and evil."
"There are certainly people and things going on in this world that are evil, and we have to be very, very concerned about them," Mr. Brennan said. "But there is no way that kinetic power [war fighting] alone is going to be able to resolve those problems. In many respects, one of Senator Obama's most impressive attributes is that he really does see the world as a three-dimensional chess board, where moves are made on one board that have implications for the other two. The world is not a game of kinetic checkers."
Mr. Brennan first met Mr. Obama about a year ago thanks to Anthony Lake, co-chairman of Mr. Obama's foreign policy advisory team.
Mr. Brennan helped prepare Mr. Lake, who was President Clinton's first national security adviser, when Mr. Clinton nominated Mr. Lake to direct the CIA in 1997. Mr. Lake's nomination was withdrawn after Republicans blocked it, but Mr. Brennan apparently made a lasting impression.
"John loves the CIA and is of the CIA," said Joan Dempsey, another former colleague.
"He was one of only a couple of people I worked with … who had the ability to love the CIA, but not be taken in by its problems and its challenges. He was never fooled; he did not believe the CIA was all powerful and all knowing; he could be of the organization but not captured by it. He has a moral compass and a professional compass that is unwavering."