Highly recommend Ghost Wars: The Secret History of the CIA, Afghanistan, and Bin Laden, from the Soviet Invasion to September 10, 2001 and the sequel Directorate S: The C.I.A. and America's Secret Wars in Afghanistan and Pakistan. They are long but very detailed and really lays out the complex relationships between the CIA, Pakistani ISI, and the various groups that came and went leading up to 9/11 in the first book, and post 9/11 in the second.

Descent into Chaos: The United States & the Failure of Nation Building in Pakistan, Afghanistan & Central Asia and In the Graveyard of Empires: America's War in Afghanistan are also great reads about Afghanistan.

Not as on topic, but still good would include The Way of the Knife: The CIA, a Secret Army, and a War at the Ends of the Earth about how the CIA shifted towards more targeting operations and the military shifted to more intelligence gathering and how that has blurred the lines between the two. And The Accidental Guerrilla: Fighting Small Wars in the Midst of a Big One about how insurgencies work, how local people are recruited and coopted by globally minded jihadists using local problems, and how a counter insurgency operation requires understanding and addressing local dynamics and issues, and breaking the connection between locally focused fighters and global jihadists.