By the time Bashar al-Assad became President of Syria in June 2000 after the death of his father, Hafez al-Assad, Shawkat was widely considered one of the most powerful people in Syria. In 2001, Shawkat was named Deputy Director of Military Intelligence, one of the main branches of the Syrian intelligence apparatus. His portfolio included liaising with militant Palestinian groups, such as Hamas and Islamic Jihad, and he was a key architect of Syria's dominance of Lebanon. After the 11 September 2001 attacks, Shawkat was a primary contact with intelligence agencies in the United States and Europe and coordinated a US intelligence operation in Syria, which was shut down after relations between the two countries irremediably deteriorated.