American intelligence on him is sketchy; the last time U.S. agents are known to have had actionable intelligence on his whereabouts was in January 2006, when they learned that he had been invited to an Islamic holiday dinner in a mud-walled compound on Pakistan’s border with Afghanistan. A Predator drone fired a salvo of Hellfire missiles at the compound, killing some 18 people, including several al Qaeda militants. But Zawahiri was not among them.

“There are indicators that some elements of the Pakistani government may be protecting Zawahiri,” says a U.S. intel official who did not want to be named discussing sensitive information. “We have reports that he’s been hanging out in Karachi for brief periods, and we just don’t think he’s going to be doing that without a lot of people knowing about it.”…

The distrust only got worse after the bin Laden raid. President Obama, fearing a leak, ordered that Pakistan be kept in the dark. The United States, in fact, expected that the Navy SEALs would bring back evidence that Pakistani intelligence was cooperating with al Qaeda. Newsweek has learned that shortly after the SEALs stormed bin Laden’s hideout, federal prosecutors were laying the groundwork to issue sealed indictments against members of the Pakistani government or anyone else they believed had aided bin Laden. The charge, according to two law-enforcement sources, would have been “harboring a fugitive terrorist.”…

If the U.S. gets Zawahiri in its sights, it won’t want to risk compromising an operation to take him out. The al Qaeda leader’s safest bet might be to hide as deep inside Pakistani territory as he can get. Riedel believes he’s probably already there. “I think the CIA would be looking for something that looks an awful lot like Abbottabad,” he says. “A safe house in an urban area near a military base. That’s been the signature of almost all of the senior Qaeda operatives who have been killed or captured.”