If you look at Zawahiri's movement in the 90's, you will notice that He and Osama failed big time in every Islamic country on the planet, as the masses never did rise up. Thus, Zawahiri and Osama went to the middle of nowhere, which would be the stans, and there too the masses didn't rise up. It doesn't matter if the Taliban magically regain control of Afghanistan when NATO withdraws, as nobody, including the Taliban factions, wants these two yahoos around. Radical Islam, as in reinstating a caliphate to rule over everybody, never was a powerful force; people are just not that into it.
Zawahiri and his group was finished long before 9/11 happened.