Michael Loccisano / Getty Images for HBO Former Targeting Officer for the CIA Nada Bakos takes part in a Q&A following the HBO Documentary Films special screening of "Manhunt."

By Robert Windrem, Investigative Reporter, NBC News

Navy SEALs may have killed Osama bin Laden, but women led them to their prey.

Women made up the majority of analysts – at one point all the analysts -- in “Alec Station,” the unit charged with finding Bin Laden, managed the ramp-up at the CIA's Counter Terrorism Center after 9-11, and participated in the interrogation, and the waterboarding, of al Qaeda suspects. They were critical to the first capture of a major al Qaeda target, Abu Zubaydah; helped find and kill Abu Musab al Zarqawi, the leader of al Qaeda in Iraq; ran "black sites," the secret CIA prisons used to interrogate terror suspects; and in the case of two senior analysts, died in an attack by al Qaeda on a CIA compound in Afghanistan.

Fran Moore, then and now the CIA’s director of intelligence, its fourth-ranking official, said she doesn’t know if there was “something explicit” about their gender that sparked the female al Qaeda hunters. “But I can say,” said Moore, “that if those individuals hadn't been working the issue, I am not confident we would've been successful.”

Some of Moore’s male colleagues are more effusive. In a speech this January, former CIA Director Michael Hayden said an "incredible band of sisters” led the search for Osama. Michael Scheuer, who ran “Alec Station,” told Newsweek last year that, “If I could have put out a sign on the door that said ‘No men need apply,’ I would have done it.”

So why are the women of the war on terror so driven, and so valuable as analysts?

Nada Bakos, the head of the targeting team that killed Zarqawi, said her team was "three quarters women," and their relentless focus on taking down Zarqawi and other al Qaeda leaders may have been influenced by a distinctly female view of security.

After 9-11, she said, the women working for her seemed to have vowed, "You're not going to do that to me again."

"We're aggressive in the protection of our children,” said Bakos. “We see risks differently, longer term."

Carol Rollie-Flynn, former executive director of the agency's Counter Terrorism Center, said she thinks “the real strengths of these women were their intense dedication and incredible attention to detail."

Nathalie Bardou / AP On May 5, 2011, four days after the raid that killed him, Pakistanis walk by the compound where al Qaeda leader Osama bin Laden was caught and killed in Abbottabad, Pakistan.

Detail and more detail, said Bakos, was a big part of the Zarqawi team’s day. The women sifted through communications intercepts, interrogation reports, snippets from human spies, and satellite images, trying to make their analysis “operational” – meaning good enough to find their target and strike him.

Whatever the intangibles, even two years before 9-11, all the staffers in "Alec Station" except Scheuer were female. After 9-11, women were involved in setting up the earliest "black sites,” and participated in the controversial interrogations themselves. Officials told NBC News that both Zubaydah and ”KSM” -- Khalid Sheikh Mohammed, the 9-11 mastermind -- were interrogated by women, sometimes with the aid of "enhanced interrogation techniques," including waterboarding, the simulated drowning technique since outlawed.

A former CIA official told NBC News that he thought women might have been especially effective at interrogating terror suspects because of the combination of surprise and shame. Jihadis were stunned that women, whom they saw as inferior, had been chosen to question them.

For the first time in the organization's history, nearly half of the CIA, including five of the top spots, is made up of women. NBC's Ann Curry looks at the history of women in the organization.

Jose Rodriquez, the head of the CIA's Counter Terrorism Center and National Clandestine Service during much of the hunt for bin Laden, said in his book “Hard Measures” that “KSM” once told one of his female interrogators that he much preferred dealing with women. According to Rodriguez, KSM said he believed women were "better prepared and less judgmental." KSM told male debriefers something different, however – that he was glad to see "the CIA wasn’t entirely run by women."

The woman with perhaps the biggest role in the hunt for bin Laden, however, wouldn’t live to see her mission completed. Portrayed as “Jessica” in “Zero Dark Thirty,” Hollywood’s take on the bin Laden raid, Jennifer Matthews had been an analyst with Alec Station in the late ‘90s, then moved to the clandestine side.

“There were a handful who formed a human database on al Qaeda and I recall they were all women," said Rollie-Flynn. "Jennifer Matthews was one of them. They knew everything. Their knowledge was encyclopedic. They would brief the director and had all the answers.”

CIA Director John Brennan sits down with NBC's Ann Curry to discuss the role women have played in the agency in his first television appearance since taking office.

In early 2002, Rodriguez appointed Matthews to head a task force tracking the elusive Zubaydah. Then pregnant with her third child, she dove into the challenge and by March had determined he was at one of 16 sites in Pakistan. Between the FBI and Pakistan’s ISI, there was enough manpower to carry off simultaneous raids on all 16, though she told National Security Adviser Condoleezza Rice that the chances for success were no better than 40 percent.

The raids were launched on March 28, 2002. Afterwards, Matthews broke into CIA Director George Tenet's 5 p.m. "threat meeting" to read a brief email from a CIA team leader in Faisalabad, Pakistan. Zubaydah had been severely wounded in a firefight and captured.

In 2008, Matthews was promoted to head a CIA station in the belly of the beast, Afghanistan. Matthews arranged for a jihadi she thought had been "turned" to meet with CIA officers and provide information on the whereabouts of bin Laden and his No. 2, Ayman al-Zawahiri. But the mole was really an assassin. Five days after Christmas 2009, he entered the CIA compound in Khost without being searched and detonated a bomb, killing himself and seven CIA officers, including Matthews and another female analyst.

Some used the tragedy to criticize Matthews, and question her skills. While defenders said the opportunity was too good for anyone to pass up, others thought she’d been blinded by seeing her quarry too close at hand and failed to follow security procedures.

The al Qaeda hunter now known to the public as "Maya" didn't escape criticism either. In “Zero Dark Thirty,” Maya, who is based on a real person, helps lead the hunt for bin Laden, grieves for the death of her mentor “Jessica,” and then demands to go to Afghanistan as the SEALs prepare to raid Osama’s lair. She watches the helicopters disappear into the darkness, knowing that her years of effort led them to their quarry.

CIA Fran Moore receives a commendation from then-CIA Director Leon Panetta.

After bin Laden’s death, the real Maya got a cash bonus and a medal. She had been crucial to the search, if not as central as her movie counterpart. But she was denied a promotion and a $16,000 pay raise -- perhaps, suggested one former CIA official, because she doesn't “play well with others. She has very sharp elbows." She is not permitted to speak to the media, and has not responded publicly to the criticism.

No one suggests that criticism is going to slow the rise of women at the CIA. As the agency moves on to other crises, women have new roles. The Syria "shop" is filled with women and a woman holds a key position in the group that tracks Iran's nuclear program. The deputy director of the National Clandestine Center, the agency's undercover arm, is a woman.

John Brennan, the current director of the agency, told NBC News women have a unique perspective.

"We all are products of our experiences," said Brennan. "In addition to the innate intelligence and capability and creativity that women bring to the workforce, I think they have the opportunity to see the world through -- and I think this is very important-- the eyes of a woman."

Slideshow: Secret Agent Ma’am Courtesy Betty McIntosh A pictorial history of America's female spies, from the OSS officers who worked behind the lines in WWII to some of today's top CIA officials. Launch slideshow

More from NBC News Investigations:

Follow NBC News Investigations on Twitter and Facebook