In 1987, he was assigned to the Defense Intelligence Agency as the assistant defense intelligence officer for the Middle East. During this assignment, he spent much of 1987 and 1988 at the U.S. Embassy in Baghdad, Iraq, as a liaison officer to the Iraqi armed forces Directorate of Military Intelligence. Francona worked an observer of Iraqi combat operations against Iranian forces, and flew sorties with the Iraqi Air Force. His observations were key to the discovery of Iraqi chemical weapons capabilities and ballistic missile modifications.