The idea that the 9/11 attacks have their roots in the Soviet-Afghan war comes from bin Laden's role in it. During much of the war he, and Ayman Al Zawahiri, the Egyptian head of Islamic Jihad, an Egyptian group, lived in neighboring Pakistan. There, they cultivated Arab recruits to fight with the Afghan mujahideen. This, loosely, was the beginning of the network of roving jihadists that would become Al Qaeda later.
It was also in this period that bin Laden's ideology, goals and the role of jihad within them developed.
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