Abu Ayoub al-Iraqi
In the 2001 trial for the 1998 bombings of U.S. Embassies in Africa, Jamal al-Fadl testified that he first met Abu Ayoub al-Iraqi at a worldwide jihad group in a meeting in Khost, Afghanistan in 1989. Al-Fadl termed him the "emir" of al-Qaeda, but clarified that he was always second to Osama bin Laden.
Abu Ayoub was replaced by Abu Ubaidah al-Banshiri as emir, apparently sometime before 1991, according to trial testimony from both al-Fadl and L'Houssaine Kherchtou. Al-Banshiri died in an accidental drowning in 1996. as L'Houssaine Kherchtou described Abu Ubaidah as al-Qaeda's second-in-command at that time. Other material suggests, however, that he was #3, since he was replaced by Mohammed Atef.