The Truman saw continuous action for over 50 days, conducting precision airstrikes and launching missiles while under constant fire from Houthi militants.
It's the latest development in the U.S. military's struggle to bring to justice the man charged with planning the Sept. 11 attacks on the United States.
U.S forces are still needed in Syria to prevent ISIS from reconstituting as a major threat following Assad's ouster, Defense Secretary Lloyd Austin said.
The decision puts back on track agreements that would have the three men plead guilty in exchange for being spared the possibility of the death penalty.
The Pentagon chief also stressed trilateral cooperation with Tokyo and Seoul is crucial for regional stability even as South Korea is in political turmoil.