Remember Raymond Davis, the "consular employee" in Pakistan who was arrested and is being held by the Pakistanis for killing two armed individuals who apparently tried to kill him? Obviously it is a lot more complicated than that snippet of a story. It is at the core of the very explosive set of disagreements between the United States and Pakistan. emptywheel at firedoglake has an excellent analysis of what has recently been published on the subject.
Davis appears to be a spy of some sort, perhaps a contractor but now claimed by the CIA in Pakistan. Were the two men he shot security agents from the Pakistani ISI? Was Davis collecting targeting information on the Taliban in Northwest Pakistan? Was there a connection between the fact that American drone strikes in North Waziristan ended four days before the shooting Davis was involved in? Did John Kerry really ferry Davis' backup team out of Pakistan when Kerry returned from Pakistan? Those individuals were apparently supposed to protect or rescue Davis and failed to do so. According to ABC they are now back in the U.S. and the Pakistani authorities really want them.
For details go read emptywheel's article. It doesn't have all the answers, but it brings to light a lot of very interesting questions.The commenters add a great deal more information.