John Brennan hasn’t always been a bureaucrat, working out of a comfortable office at the White House. An Arabic speaker and Saudi expert, the 57-year-old CIA director-designate has at various points in his career confronted Iranian intelligence officials and Saudi princes, briefed President Bill Clinton, camped out with Bedouins in the Arabian desert and helped create the agency that ultimately became National Counter Terrorism Center.

Known now as President Barack Obama’s chief counterterrorism adviser, Brennan spent most of his career in the CIA.   

A working-class kid from Hudson County, N.J., best known for its political intrigue, Brennan decided at a young age to apply for a job in international intrigue after graduating from Fordham University -- and reading a classified ad in the New York Times seeking recruits for the CIA.

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He joined the agency in 1980, and for the next 25 years he worked for the CIA, both in Washington and overseas. He got his big career break when he was noticed by George Tenet in the mid-1990s. He was at the time delivering the agency’s security briefings to then-President Clinton.

Tenet was then intelligence adviser to the National Security Council and met with Brennan regularly on intelligence matters. When Tenet then became deputy CIA Director in 1995, he made Brennan his executive assistant. Then, when John Deutch abruptly quit as CIA director in 1996, Tenet succeeded him first on an interim basis, then permanently. Brennan, who was in Saudi Arabia from 1996-'99, returned to become Tenet's chief of staff, his gatekeeper on the CIA's seventh floor.   

Obama taps Brennan to be next CIA director

Brennan's knowledge of Arabic and Arab cultures made him indispensable to Tenet in many ways and, in 1998, Tenet appointed him station chief in Saudi Arabia.

Work in Iran, with Saudis
In his memoir, "At the Center of the Storm," Tenet recounts a number of incidents where Brennan used his wits to get a message across.

Perhaps the most memorable took place in the late 1990s, when attacks against Western targets by Hezbollah and its chief backer, the Iranian Ministry of Intelligence and Security (MOIS), were causing problems for Washington in the Mideast. The CIA decided to launch a "disruption campaign" to let both know the U.S. was aware of their actions, and try to embarrass the Iranians.

As part of the campaign, agency officers would approach MOIS officers on the street or wherever they could get close and ask them if "they would like to come to work for us or sell us information," as Tenet put it.

"In one memorable example," Tenet recounts, "John Brennan, our liaison to the Saudis, handled the local MOIS head himself.

"John walked up to his car, knocked on the window, and said, 'Hello, I’m from the U.S. Embassy, and I’ve got something to tell you.' As John tells the story, the guy got out of the car, claimed that Iran was a peace-loving country, then jumped back in the car and sped away.

"Just being seen with some of our people might cause MOIS officers to fall under suspicion by their own agency. The cold pitches undoubtedly ruined some careers, and maybe even lives, but also occasionally paid off in actual intelligence dividends. It couldn’t happen to a nastier bunch of people."

Brennan also had to deal with often-recalcitrant Saudi leaders who were not as aggressive in cracking down on Islamic militants as the U.S. wanted. 

Tenet wrote that in 1998, the Saudis had thwarted an al-Qaida operation in the kingdom. Their intelligence serviced had learned that operatives for the terror group were planning to smuggle four Sagger anti-tank missiles into the country from Yemen. What troubled the CIA was that the Saudi intelligence service had not informed the U.S. government of the plot. Even more troubling was the timing of the plot – just days before then-Vice President Gore was set to visit the kingdom. It didn't take much analysis to persuade the CIA that the missiles were part of an assassination plot. 

The lack of cooperation set off alarm bells at CIA headquarters in Langley, Va. If the Saudis weren't going to inform the CIA about such an explicit threat, what would they inform the U.S. about?

Brennan was instructed to meet with Prince Turki bin Faisal, then head of Saudi intelligence. Turki pleaded ignorance and so Brennan suggested that Tenet pay a visit and play a bit of hard ball with the Saudis.

At Brennan's suggestion, Tenet met with the late Prince Nayef bin Abdulaziz Al Saud, the royal in charge of security. After what seemed to be an interminable soliloquy by the prince on the two countries' "special relationship," Tenet interrupted and, to get Nayef’s attention, moved in close and put his hand on the prince's knee, something one does not do with a Saudi royal.

Tenet then delivered his message to Nayef. "I let him go at last, but I assured him that I would be back the next week, and every week after that if necessary, to ensure that the flow of terrorism-related information between U.S. and Saudi officials was timely and unencumbered," he wrote.

Within a week, Brennan was given a comprehensive written report on the Sagger episode by the Saudis, for which he expressed profound gratitude.

Enhanced interrogation 'saved lives'
In other negotiations between Tenet and Arab leaders, Brennan was often one of two or three advisers in the CIA director's party. 

In one memorable meeting with Yasser Arafat, Tenet writes that he had Brennan vet a proposed peace agreement between the Palestinian Authority and Israel before presenting it to the Bush White House, wanting his expert eye to review it. 

After Brennan’s return to Washington from Saudi Arabia 2002, Tenet made him deputy executive director of the CIA. The job took him out of intelligence gathering and into administration. As the No. 2 in the CIA's administrative office, Brennan was essentially "deputy mayor" of the agency, "making the trains run on time" for the worldwide operation, as one former Tenet aide put it.

In that role, he helped set up the Terrorist Threat Integration Center, the predecessor to the National Counter Terrorism Center. Brennan built the unit from the ground up, finding the building, setting up security procedures and staffing it with analysts from across the intelligence community. His aggressiveness in staffing didn't sit well with those who lost analysts. In his memoir, "Hard Measures" Jose Rodriguez, then the director of the CIA's Counter Terrorism Center, accused Brennan of "ripping most, if not all, of the top CT (counter terror) analysts out of CTC."

But after creating the organization, he was passed over for director of the NCTC and left the government in 2006, founding The Analysis Corp., an intelligence contractor with offices near the NCTC offices. In 2008, he joined Barack Obama's presidential campaign as intelligence adviser.

There's no indication Brennan played a role in development of the CIA's "enhanced interrogation techniques," which were established in 2002 and 2003 while he was in the CIA's administrative office. 

Brennan later said he opposed some of the most egregious interrogation techniques. Waterboarding, for instance, was "not going to be allowed under an Obama presidency," he told The Washington Times in 2008, just before the presidential election.

But when President-elect Barack Obama floated Brennan’s name to be CIA director, controversy over the enhanced interrogation techniques was increasing and Brennan came under attack from the left. Although his fingerprints weren't on the memos that established the interrogation program, his tacit support for them became a problem. Glenn Greenwald, writing for Salon.com, called Brennan "an ardent supporter of torture" and "one of the most emphatic advocates" for enhanced surveillance powers.

Opponents of his nomination also pointed to an interview with Harry Smith, then of CBS News, in September 2007. 

Brennan defended the techniques as necessary. "There (has) been a lot of information that has come out from these interrogation procedures that the agency has in fact used against real hard-core terrorists. It has saved lives," he told Smith emphatically. "And let’s not forget, these are hardened terrorists who have been responsible for 9/11, who have shown no remorse for the deaths of 3,000 innocents."

In the interview, Brennan also defended Attorney General Michael Mukasey, who in his Senate confirmation hearing had refused to call the enhanced interrogation techniques “torture.”

'Tireless,' 'legendary'
The criticism took its toll, and less than three weeks after the election, Brennan withdrew his name from consideration.

"It has been immaterial to the critics that I have been a strong opponent of many of the policies of the Bush administration, such as the pre-emptive war in Iraq and coercive interrogation tactics, to include waterboarding," he said in a Nov. 25, 2008, letter to Obama.

Instead, Obama named him his counterterrorism adviser. In that role, he pushed hard for finding al-Qaida leader Osama bin Laden and originally was a champion of the CIA’s drone program in Pakistan, which has become a centerpiece of Obama’s anti-terror operations there. But in recent months, according to several reports, he was leading a drive to put more controls on targeting, among other things.

While Brennan has his critics inside and outside the agency, none questions his work ethic and toughness.

As Obama said Monday, “In all this work, John has been tireless. People here in the White House work hard, but John is legendary, even in the White House, for working hard.”

As for his toughness, one former colleague recalled that while working at the White House, Brennan had a hip replaced on a Monday and was back at work on Thursday. The colleague said he was told that the next time Brennan went in for a hip replacement operation, the driver who took him to the hospital asked if he should wait.  

Robert Windrem is a senior investigative producer for NBC News.

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White House counterterrorism adviser John Brennan on Monday spoke openly -- and at great length -- about what has long been one of the government’s most controversial official secrets:  the use of remotely piloted drones to kill suspected terrorists.

In doing so, he became the first U.S. government official to acknowledge that the drone strikes sometimes kill innocent people, though he characterized such deaths as  “exceedingly rare.” But a new analysis by an independent Washington think tank estimates that more than 300 civilians have been killed by drones since President Barack Obama took office.

In a major speech on the anniversary of Osama bin Laden’s death during a raid in Abbottabad, Pakistan, by U.S. Navy SEALs, Brennan proclaimed that al-Qaida is now "on the path to its destruction."  But the headline was what he had to say about the drone program — long a forbidden subject for senior U.S. officials  — and how the U.S. government uses it.

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“The United States conducts targeted strikes against specific al-Qaida terrorists, sometimes using remotely piloted aircraft, often referred to publicly as drones,” said Brennan, in his speech at the Woodrow Wilson International Center for Scholars, a Washington, D.C., foreign policy think tank.  

While it has been openly reported in the press for years, the use by the CIA of pilotless drones to kill members of al-Qaida has long been officially classified,  prompting government officials to talk obliquely about “lethal operations” and “removal” of terrorists. They have done so even as Obama has dramatically escalated the number of such attacks and made them the central component of the administration’s counterterrorism efforts.

One U.S. intelligence official, speaking on condition of anonymity, told NBC News that the speech represents “a pretty big sea change for us” in terms of what officials will now be permitted to talk about. But the official said that while Brennan’s speech had been carefully vetted throughout the U.S. intelligence and national security community, there had been no formal declassification of the drone program. “The president can declassify anything he wants,” said the official, adding that Brennan – as the representative of the president — can speak about anything his boss wants him to discuss.   

Under Obama, there have been an estimated 250 drone strikes in northwest Pakistan that have killed as many as 2,345 people, according to an analysis by the New America Foundation, a Washington think tank that closely tracks the program. Such strikes have generated a storm of protest in Pakistan and stepped up demands by the Pakistani government to halt them.   

In what he described as an effort to be more open with the American people, Brennan on Monday described an elaborate process under which senior government officials select targets for drone strikes. They must first determine whether a prospective target is a bona fide member of al-Qaida or “associated forces” and poses a “significant threat” to U.S. interests.  The “lethal action” strikes are not used for “punishing terrorists for past crimes” or “seeking vengeance.” Instead, they are used to “stop plots” and “prevent future attacks,” citing as one example, targeting individuals  who possess “unique operational skills.”

Read more reporting by Michael Isikoff in 'The Isikoff Files'

Brennan  said the use of drones gives U.S. intelligence agencies the ability to use “laser-like” precision against the terrorists. But he acknowledged that "innocent civilians have been killed in these strikes." He said such instances have been "exceedingly rare, but it has happened.

“When it does, it pains us and we regret it deeply, as we do any time innocents are killed in war," he added. 

That passage of his speech alone was significant. In June 2011, Brennan said that in the previous year of operations in the government’s then-unspecified program to eliminate al-Qaida members, “There hasn’t been a single collateral death because of the exceptional proficiency, precision of the capabilities we’ve been able to develop.”   

Brennan later changed that statement in response to questions by the New York Times, spurred in part by  reports about a May 6 strike in Pakistan that  hit a religious school, an adjourning restaurant and a house, killing 18 people. Although 12 militants were allegedly killed, British and Pakistani journalists on the scene reported that six civilians also died in the strike.

In Brennan’s adjusted statement last year, he said, “Fortunately, for more than a year, due to our discretion and precision, the U.S. government has not found credible evidence of collateral deaths resulting from U.S. counterterrorism operations outside of Afghanistan or Iraq.”

Brennan did not give any details on Monday about how rare civilian deaths have been. But according to the analysis by the New America Foundation, which relies heavily on local media and other reports from observers in Pakistan, about 17 percent of those who have been killed by drones since the program effectively began in 2004 were “non-militants.”  The foundation estimated that the  “non-military fatality rate” has since dropped to about 13 percent under Obama – as drone strikes have become more frequent and more precise.

Those numbers translate to 471 civilian deaths, including 309 under Obama.

Human rights groups — who have challenged the administration to be more open about its drone program — were not satisfied with the new details provided by Brennan’s speech.

“It is not enough that care is taken to avoid harm to innocent civilians,” said Raha Wala, an official with Human Rights First. “Brennan's assertion that any 'member' of al-Qaida or 'associated forces' is legally targetable is wrong. Under the laws of armed conflict, only members of the enemy's armed forces, or those directly participating in hostilities or who perform a continuous combat function, may be targeted.”

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