If you have time to read only one book on Afghanistan, the hands-down choice is Ghost Wars: The Secret History of the CIA, Afghanistan and Bin Laden from the Soviet Invasion to September 10, 2001 by Steve Coll. If you have time to read two, then The Places In Between by Rory Stewart also is fantastic.
While the scope of Ghost Wars is obvious from the title, its depth is astonishing. Coll, a former WaPo journalist who now blogs for The New Yorker, among other things, explains how the CIA blew hot and cold on Afghanistan, failed to anticipate the emerging power of the Taliban, and along with the FBI anticipated the 9/11 attacks but failed to act on, let alone share the intelligence that they gathered.
Ghost Wars was published in 2004, but remains the best book on the run-up to the attacks on the World Trade Center and Pentagon.
In January 2002, only weeks after the U.S.-led invasion, Stewart looked death in the face and walked across Afghanistan, following the path taken by Babur, the country's first Mughal emperor.
The account of this Scotsman, who now teaches at Harvard's Kennedy School, is alternately heartfelt and humorous. His knowledge and understanding of the Afghan people and their customs, allegiances and history is an intimate counterpoint to Ghost Wars and the best ground-level account of the fiercely proud denizens of that war-ravished land.