The hearing was interrupted repeatedly — once before it began and then several times before Brennan had completed his brief statement. At one point, Sen. Dianne Feinstein, D-Calif., ordered the proceedings halted and the room cleared so those re-entering could be screened to block obvious protesters.
The shouted protests centered on CIA drone strikes that have killed three American citizens and an unknown number of foreigners overseas.
It was a topic very much on the mind of the members of the Senate Intelligence Committee who eventually will vote on Brennan's confirmation.
In the hours before the hearing began, President Barack Obama ordered that a classified paper outlining the legal rationale for striking at U.S. citizens be made available for members of the House and Senate intelligence panels to read.
It was an attempt to clear the way for Brennan's approval, given hints from some lawmakers that they might hold up confirmation unless they had access to the material.
In his opening statement, Brennan said, "The need for accurate intelligence and prescient analysis from CIA has never been greater than it is in 2013 — or that it will be in the coming years."
He said historic transformations continue sweeping through the Middle East and North Africa, with "major implications for our interests, Israel's security, our Arab partners and the prospects for peace and stability throughout the region."
Additionally, Iran and North Korea "remain bent on pursuing nuclear weapons and intercontinental ballistic missile delivery systems," he noted.
He said the United States remains at war with al-Qaida and its associated forces, which he said seek to "carry out deadly strikes against our homeland and our citizens as well as against our friends."
As for U.S. computer systems, he said they are under daily attack by "nation states, international criminal organizations, subnational groups and individual hackers."
Brennan is a veteran of more than three decades in intelligence work, and most recently served as Obama's top counter-terrorism adviser in the White House. Any thought he had of becoming CIA director four years ago vanished amid questions of the role he played at the CIA when the Bush administration approved waterboarding and other forms of "enhanced interrogation" of suspected terrorists.
White House spokesman Jay Carney said Wednesday the White House is making "extraordinary accommodation" in allowing lawmakers to view classified Justice Department legal advice on drone strikes against Americans. Carney said the White House does not plan to send the Justice memos to lawmakers beyond those on the House and Senate intelligence committees.
Sen. Ron Wyden, D-Ore., a committee member who had pressed the administration to provide the legal opinion, left open the possibility he might still try to block Brennan's nomination. But he said turning over the opinion was a good first step.
"I'm committed to making sure that we get all the facts," Wyden said on NBC's "Today" show. "Early this morning, I'm going to be going in to read the opinion. We'll go from there."
Wyden said "there are still substantial questions" about how the administration justifies and plans drone strikes. "The Founding Fathers thought the president should have significant power in the national security arena. But there have to be checks and balances," Wyden said. "You can't just skirt those checks and balances if you think it's inconvenient."
An unclassified memo leaked this week says it is legal for the government to kill U.S. citizens abroad if it believes they are senior al-Qaida leaders continually engaged in operations aimed at killing Americans, even if there is no evidence of a specific imminent attack.
Brennan laid out the administration's policy for targeting al-Qaida with lethal drone strikes ahead of the hearing, defending the use of such strikes but disavowing the harsh interrogation techniques used when he was at the CIA.
In answers to pre-hearing questions released Wednesday by the Senate Intelligence Committee, Brennan said no further legislation was necessary to conduct operations against al-Qaida wherever it's operating.
He also answered some of his critics who charged him with backing the detention and interrogation policy while he served at the CIA. Brennan said in his written answers that he was "aware of the program but did not play a role in its creation, execution, or oversight." He added that he "had significant concerns and personal objections" to the interrogation techniques and voiced those objections privately to colleagues at the agency.
Brennan went on to describe how individuals are targeted for drone strikes, saying whether a suspect is deemed an imminent threat — and therefore appropriate for targeting — is made "on a case-by-case basis through a coordinated interagency process" involving intelligence, military, diplomatic and other agencies.
Human rights and civil liberties groups have decried the methods for targeting terror suspects, especially U.S. citizens.
Brennan defended the missile strikes by unmanned Predator or Reaper drones as a more humane form of war, but he acknowledged "instances when, regrettably and despite our best efforts, civilians have been killed."
"It is exceedingly rare, and much rarer than many allege," he added.
Aides have portrayed Brennan as cautious in the use of drones, restraining others at the CIA or military who would use them more often, even though as the White House's counterterror adviser, he has presided over an explosion of drone strikes in Pakistan, Yemen and Somalia. Fewer than 50 strikes took place during the Bush administration, while more than 360 have been launched under Obama, according to the website The Long War Journal, which tracks the operations.
Administration officials say Brennan would further limit the use of drones by the CIA and leave the majority of strikes to the military. Brennan signaled in his written answers that he would not seek to expand the CIA's paramilitary operations.
"While the CIA needs to maintain a paramilitary capability ... the CIA should not be used, in my view, to carry out traditional military activities," Brennan wrote, referring to activities like the special operations raid that killed al-Qaida leader Osama bin Laden.
The CIA's drone strikes primarily focus on al-Qaida and Taliban targets in the tribal regions of Pakistan, while the military has launched strikes against al-Qaida targets in Yemen and Somalia. The agency also carries out strikes in Yemen, where three American citizens with al-Qaida connections have been killed: Anwar al-Awlaki, his 16-year-old-son and Samir Khan.
Brennan said he would work to improve the CIA's intelligence collection and performance across the Arab world after a spate of unanticipated unrest, from the revolts of the Arab Spring to the terror attack that killed the U.S. ambassador and three other Americans in Benghazi, Libya.
Brennan will also face questions about charges that White House officials leaked details of the administration's national security policies, including its cyberattacks against Iran's nuclear infrastructure, to burnish Obama's standing as commander in chief ahead of last year's presidential election.
Brennan told the Senate committee that he was questioned as a voluntary witness in a leaks investigation the White House launched in response to congressional anger.
He also said that in his current role, he is "vigilant about not disclosing classified intelligence matters with unauthorized persons" but added that "in exceptional circumstances ... it may be necessary to acknowledge classified information to a member of the media or to declassify information for the very purpose of limiting damage to national security."