Legendary Spy Charlie Allen Knows the CIA's Secrets

Nearly 20 years later, when Saddam Hussein deployed the Iraqi Army near Kuwait's border, Allen wouldn't made the same mistake again. He was the national intelligence officer for warning, akin to the CIA's chief sentry. For several weeks that summer, he sent out a series of alerts about a pending invasion, culminating in an official "warning of war" message. But he was largely ignored. When Allen's last warning reached the State Department, analysts there dismissed it as typical CIA exaggeration. A few hours later, Iraq invaded Kuwait. "People either dislike Charlie or they admire him, and for the same reason—he's usually right," says Richard Clarke, a longtime colleague and a former presidential counterterrorism adviser.

This incident was a prelude to one of the most difficult moments in Allen's career. In 1991, six weeks into the air campaign against Iraq, he was working with Air Force planners to select targets. Allen and his CIA colleagues were suspicious of a building called Public Shelter No. 25, in the Amiriyah neighbor-hood of Baghdad. According to CIA maps, it was a secret operations center used by the Mukhabarat, Iraq's intelligence service. At Allen's urging, the Air Force dropped a pair of laser-guided bombs on the bunker.

Hundreds of civilians who had taken cover inside were killed. "It was a very difficult moment. We thought it was Mukhabarat, and there were some there," Allen says, casting his eyes to the ceiling. "But we did kill innocent people, a lot of them," he adds after a short pause. "I carry those lessons around every day, but I never lost heart or a sense of mission."

By 1998, Allen was spending more and more time on terrorism issues. Then CIA Director George Tenet tasked him to coordinate the intelligence community's efforts against Osama bin Laden, whose organization bombed two U.S. embassies in Africa that August. Allen and Clarke set up a meeting of the nation's top al Qaeda experts and came to the conclusion that bin Laden's most likely hiding place was an Afghan valley where U.S. spy satellites could not peek into the caves. The area was called Tora Bora, which later became famous when al Qaeda leaders took refuge there after the invasion of Afghanistan in 2001.

Two years later, frustrated by the lack of intelligence about bin Laden, Allen walked into Clarke's White House office holding a picture of a small unmanned aircraft. "Ever heard of something called a Predator?" he asked. Allen said that getting the Predator deployed over Afghanistan was "a bloody struggle," but in the fall of 2000, one of the drones captured hours of video footage of a tall, bearded man who analysts believe was bin Laden. For the next year, Allen fought to arm the Predator with missiles. "We need to hit him," Allen told colleagues in the summer of 2001, "before he hits us." Weeks after the 9/11 attacks, armed drones were finally deployed, and today they are one of the chief weapons against al Qaeda targets in Afghanistan and Pakistan.

By this time, Allen was coordinating collection efforts for the entire intelligence community. First for the director of central intelligence and later for the new director of national intelligence, his job was to determine how to deploy a network of spy satellites, eavesdropping sensors, and human spies to go after targets from terrorists to nuclear-armed dictators. He called it being "the night watch for central intelligence." The post came with limited authority, but the man dubbed "Charging Charlie" by colleagues wielded his formidable reputation to get things done. "When Charlie Allen comes to you demanding answers, you got them," says retired CIA veteran Robert Grenier. "He is unique in the agency because he commanded so much respect."

Though Allen speaks excitedly about his final government job—running the nascent intelligence office at the Department of Homeland Security—others say it was a thankless assignment. "I never felt that I was just part of the bureaucracy," he says. "You can't assume all the world's burdens, but if you have a sense of mission for keeping the country safe, one person can make a difference." DHS was in chaos when Allen arrived in 2005. He brought along some CIA colleagues to help manage intelligence analysis and began coordinating the efforts of countless other agencies, from local police departments to the Coast Guard. Even though he never figured out how to stop getting pulled aside for additional screening at airport checkpoints, Allen says that DHS and the nation have become more sophisticated at dealing with the threat of terrorism since 9/11. Of course, the work remains unfinished. "We have learned," he says, "to take nothing for granted."