Za Zawahirija, za čiji se EIJ kaže da se s el-Kaidom udružio 1998, također se smatra da je jedan od glavnih planera samoubilačkog bombaškog napada na brod USS Cole u blizini obale Jemena 2000. godine, te "mozak" iza napada na Sjedinjene Države od 11. septembra.
Zawahiri, whose EIJ is said to have merged with al-Qaeda in 1998, is also believed to have been one of the masterminds of the suicide bombing of the USS Cole off the coast of Yemen in 2000, and the "brains" behind the September 11th attacks on the United States.