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.
Zavahiri, čiji se EIJ, kako se misli, spojio sa Al Kaidom 1998, takođe je, veruje se, jedan od glavnih planera samoubilačkog bombaškog napada na američki razarač US Kol kod obale Jemena 2000. godine i „mozak“ koji stoji iza napada 11. septembra u Sjedinjenim Državama.