CIA veteran John Brennan was an early lightning rod for President-elect Obama after word got out that he was being considered for the agency's top job. (Brennan had advised Obama on intelligence and foreign policy during the campaign.) The primary complaint was Brennan's past statements in defense of the CIA's practice of "rendering" terrorism suspects to other countries for interrogation—places where harsh interrogations go far beyond waterboarding. In 2006, he told a reporter that "we do have to take off the gloves in some areas," but went on to say that it must be done in a way doesn't "forever tarnish the image of the United States abroad."
Since 2005 Brennan has been CEO of the Analysis Corporation, which advises the federal government and private companies on counterterrorism. The firm's parent company, London-based Global Strategies, has come under fire for its activities in Iraq and Afghanistan, where it hired Third World private security contractors at cut rates and once shut down Baghdad's airport for several days during a contract dispute with the Iraqi government.
Obama has been critical both of the CIA's practice of rendition and the unregulated use of private security contractors in conflict zones, but seems satisfied that Brennan has not been tarnished by his connection to either one. Dropping him from consideration for CIA director (instead picking Leon Panetta), Obama went on to tap Brennan to be his top advisor on counterterrorism—a position that does not require congressional approval.
While by virtue of his position at the CIA Brennan was a part of the Bush administration's version of the war on terror, it's clear that he's broken with the outgoing administration on at least one crucially important subject: the US relationship with Iran. Last year, he contributed a policy paper (.pdf) to the Annals of the American Academy of Political and Social Science, calling for a new approach to engaging Iran. His main points:
After nearly three decades of antagonistic rhetoric and diplomatic estrangement between the United States and Iran, the next president has the opportunity to set a new course for relations between the two countries. When the next president takes up residence at 1600 Pennsylvania Avenue, Iranian officials will be listening. The president must implement a policy of engagement that encourages moderates in Iran without implying tolerance for Tehran's historic support of terrorist activities. This strategy will require patience and sensitivity to the complex political realities inside Iran. To successfully chart a new course for U.S.-Iranian relations, the next president must (1) tone down rhetoric; (2) establish a direct dialogue with Tehran, including comprehensive, private discussions and deployment of a special envoy; (3) encourage greater assimilation of Hezbollah into Lebanon's political system; and (4) offer carrots in addition to sticks, including consideration of legitimate Iranian concerns on regional security issues.
Brennan's positions align perfectly with Obama's emerging approach, down to the appointment of a special envoy to spearhead a new diplomatic relationship with Tehran: word is that incoming Secretary of State Hillary Clinton will assign veteran diplomat Dennis Ross the Iran portfolio. Whether any of this will work, though, remains an open question, reliant in large part of how Iran reacts to Obama's overtures.