Zawahiri has been second only to UBL for as long as I can remember. Certainly well before 9/11 and the WOT began.
Okay. He has been in charge, then, assuming OBL's life status has been in doubt, since 15 Dec 2001. But OBL's son has been the head of Alqaida since Jan 2002, and he has been in Iran all along.
Actually Zwahiri was a founder of Egyptian Islamic Jihad and was bin laden's mentor..