The chances are high -- astronomically high -- that the Senate will confirm John Brennan's nomination as the CIA director. But Brennan may face tougher-than-expected questions from the senators on everything from drones to torture to leaks that exposed one of America's only undercover agents in al-Qaida.

As perhaps the President's most important national security aide, Brennan has been a key general in the shadow wars that the U.S. has been fighting around the globe during the first Obama administration. He's also been in a position to disclose secrets surrounding those espionage, sabotage and paramilitary operations. And many of those secrets have in recent months leaked out into the public.

Of particular concern to some intelligence committee senators is a teleconference that Brennan held with TV counterterror pundits on May 7, after the U.S. foiled an attempt by al-Qaida in the Arabian Peninsula to detonate an underwear bomb. According to Reuters, Brennan said during the call that the attack was never a major threat, because the U.S. had "inside control" over the plot. Commentators took that to mean that the American government had a double agent within the terror group, and talked about a likely U.S. mole on television. That effectively ended what was arguably the most successful human intelligence operation against al-Qaida in 11 years since 9/11. The double agent had to be pulled from the terrorists' ranks.

It wasn't the only leak. White House officials began disclosing details -- sometime erroneous details -- about the raid on Osama bin Laden's compound just hours after the terror leader's death was confirmed. Over the late spring and early summer of 2012, minutiae about how the White House selects its targets for robotic assassination began appearing in newspapers and books. According to one of those books, Dan Klaidman's Kill or Capture, Brennan was one of three men at the center of that decision-making process, along with Vice Chairman of the Joint Chiefs of Staff Gen. "Hoss" Cartwright and the President himself. "The three form[ed] a kind of holy trinity or targeted killings," Klaidman writes.

Then unnamed U.S. officials told The New York Times that the American government was behind the wave of cyber attacks sabotaging the Iranian nuclear effort. Both the President and Brennan publicly railed against the leaks. Senate intelligence committee chair Dianne Feinstein called for hearings into the leak. The Justice Department launched an investigation, which continues to this day.

White House national security spokesman Tommy Vietor says there's no way Brennan could've been behind the disclosures. "Everyone who works with John Brennan knows he is a straight shooter who would never harm national security," Vietor told Politico. "At the White House, John has worked to prevent the publication of information that would harm our national security."

But some senators aren't completely satisfied by the assurances. "The national security leaks during President Obama's first term were worrisome and should be a topic for Mr. Brennan’s nomination hearing," emailed Brooke Sammon, the spokesperson for Florida Republican Sen. Marco Rubio, who sits on the intelligence committee.

Sen. John Cornyn, a Texas Republican who is not on that committee, went even further, saying in a statement that "John Brennan has not been absolved of responsibility for the slew of high-level security leaks that have characterized this White House. This investigation needs to be resolved before his nomination can move forward." Other senators are alarmed by things Brennan hasn't said -- like Lindsey Graham, who said the White House needs to disclose who excised a reference to al-Qaida from the CIA's talking points on the Benghazi attack before taking up Brennan's nomination.

While some senators are expressing discomfort with the disclosures about America's shadow wars, few have signaled problems with the conduct of those clandestine campaigns. Maine Republican Sen. Susan Collins is the exception: she said in a statement that she intended to query Brennan on "the increasingly paramilitary activities of the spy agency, such as the use of armed drones," which has also concerned former CIA directors.

Most senators on the intelligence panel queried for this piece either did not bring up the drone strikes or the broader counterterror campaign as a factor for Brennan's confirmation. One of the few who has, former chairman Jay Rockefeller, put out a statement praising Brennan for "know[ing] the counter-terror challenges we face, and I look forward to discussing with him the crucial legal, strategic, and oversight considerations pertaining to the CIA's counter-terror operations." Rockefeller, a West Virginia Democrat, did not mention the drones explicitly, and said he had "high expectations for John's leadership" of the CIA.

Some of Rockefeller's fellow Democrats on the intelligence committee weren't so effusive. But their concerns stem less from Brennan's tenure in the White House -- and more from his time as chief of staff of the CIA during the first George W. Bush administration. It's during that period that CIA interrogators tortured detainees in a flawed attempt to gain information about al-Qaida.

"I have questions about how he would lead the CIA and what changes he would embrace in light of the committee's problematic findings about the agency's detention and interrogation program," Sen. Mark Udall, a Democrat from Colorado and one of the panel's main civil libertarians, said in a statement emailed to Danger Room. Udall is referring to an extensive and still-classified report into CIA torture, four years in the making, that the committee completed in December. That report may be the biggest stumbling block Brennan faces before the CIA veteran can return to Langley.

"Although I cannot disclose those classified findings," Udall added, "I am troubled by them, and I believe Coloradans would be too."

Udall spokesman Mike Saccone clarifies that Udall isn't opposing Brennan at this point. Like many of his colleagues on the panel, he's reserving judgment until he hears more from Brennan. (Fellow committee civil libertarian Sen. Ron Wyden declined repeated requests to comment for this story.)

Were it not for concerns about torture, Brennan, a longtime CIA veteran, would probably already be CIA director. In 2008, after human-rights advocates focused on comments Brennan made seemingly defending torture, such as a 2007 CBS interview when he claimed the agency's "enhanced procedures...saved lives" and obtained "a lot of information." Brennan, denying he was pro-torture, preemptively informed President-elect Obama that he wouldn't take a senior intelligence position -- and, ironically, wound up with a vastly powerful White House job overseeing counterterrorism, intelligence and homeland security that was exempt from congressional oversight.

Now those concerns have returned -- centering not just around Brennan's attitudes towards torture, but what he might have done about it. Brennan served as deputy executive director of the CIA and a top lieutenant of Director George Tenet after 9/11, when the CIA established its torture methods. Sen. Feinstein praised Brennan as a "strong and positive director," but pointedly noted that she'll ask Brennan for his response to the "Intelligence Committee's recently completed report on CIA detention and interrogation operations from 2001 to 2009." So did Sen. John McCain, an honorary but non-voting member of the panel and a torture survivor, who questioned Brennan's possible role in torture and his "his public defense of those programs."

The committee report remains classified. But Greg Miller of the Washington Post tweeted that the report finds Brennan was "read into [the] CIA interrogation program," but "wasn't making decisions about it. (nor did he apparently object)." Miller added that the White House "pored" over the report to ensure it didn't implicate Brennan sufficiently to derail his nomination.

Brennan was also involved in another post-9/11 CIA controversy, one that's gotten far less notice. In 2003 and 2004, according to journalist Aram Roston, Brennan passed bogus CIA intelligence to the White House claiming that al-Qaida had secretly embedded information about upcoming attacks into al-Jazeera broadcasts. The false reports allegedly contributed to the Bush administration raising the terror threat level in 2003 and canceling international flights. Former CIA counterterrorism chief Jose Rodriguez told Roston that Brennan was a "major factor" in keeping the "ridiculous" intelligence alive. On the other hand, Vietor denied to Roston that Brennan was central to the incident, and Rodriguez may have an axe to grind with Brennan, since Rodriguez was a major figure in the CIA torture efforts that Obama repudiated.

After leaving government in 2005 to run an intelligence contracting firm, The Analysis Corporation, Brennan indeed made statements defending the agency's torture efforts, though he also criticized the mock drowning known as waterboarding for being "inconsistent with American values." That's part of a pattern throughout Brennan's time out of government: defending the CIA and controversial intelligence practices against their critics. In 2006, National Security Agency director Michael Hayden, the architect of the Bush administration's warrantless surveillance efforts, was nominated to run CIA. Brennan, who said he was "intimately familiar" with the surveillance program, defended Hayden as "dedicated to defending the Constitution" during a Washington Post live chat. At another point in the chat, Brennan threw a jab at the Defense Department's "growing role in intelligence matters," a reflection of Brennan's earlier efforts under Tenet to stave off former Defense Secretary Donald Rumsfeld's bureaucratic push into the intelligence world.

When Tenet released his memoir the following year, former aide Brennan feted him for a book signing at the Analysis Corporation's McLean, Virginia campus. A May 2007 press release cited Brennan celebrating the attendance of over 600 current and former intelligence officials and their families for an event so packed that Tenet signed books "for almost seven hours."

Brennan's time at the Analysis Corporation provided him with a venue to maintaining his ties to the agency. It provided the intelligence community with software designed to ease database searches. Products Brennan inherited, like Fuzzy Finder, were "designed to match inconsistent, incomplete, or erroneous alphanumeric data," according to company literature; similar legacy software, like "Arabic Name Search" and "Russian Name Search" were data-mining tools for counterterrorism analysts. Announcing a 2006 corporate partnership with the software firm Infoglide, Brennan beamed that the combined software packages would provide a "powerful analytic solution to complex challenges." After it was learned that the 2009 would-be Christmas bomber Umar Farouk Abdulmutallab slipped through a vast analytic dragnet, in part because keyword searches at the National Counterterrorism Center couldn't properly account for different English transliterations of Abdulmutallab's name, Brennan had to get a special White House waiver to lead an investigation into government watchlists, since some involved his former company's software.

Nearly every Senate aide interviewed for this piece said their bosses were reserving judgment on Brennan, even those who expected his confirmation hearing to turn significantly on the question of torture. There may be another irony around that. Feinstein isn't immediately declassifying the Senate report; she's sending it to the executive branch for prior review before the panel considers declassification. That gives the Obama administration an interest in withholding a supposedly damning report that could embarrass its pick for CIA director. Even if Brennan didn't aid torture, his nomination could inadvertently keep his agency's legacy of torture in the shadows -- next to its drone fleet.