On June 7, 1798, he was appointed as
Captain in command of , during the
Quasi-War with
France and made several successful captures of French vessels. At the reduction of the US Navy after the war with France, Morris was retained as fifth in rank and recalled to command the
Mediterranean Squadron in 1802 during the
First Barbary War. In command of , Morris led an unsuccessful blockade of
Tripoli, mostly remaining in
Gibraltar for the better part of 1803. Morris was relieved of duty and command of the squadron would turn over to
Edward Preble in . Recalled to the United States, Morris faced a
court of inquiry which decided that he had not "discovered due diligence and activity in annoying the enemy". On May 16, 1804,
Secretary of the Navy Robert Smith, with the agreement of President
Thomas Jefferson, revoked his captaincy in the U.S. Navy and dismissed him from the service. Morris had brought his wife and young son on board with him and was accused of taking actions "more reflective of a concerned husband and father than a military commander in the midst of a war."
Political career From July 1, 1813 until June 30, 1814, Morris was a
Federalist member of the
New York State Assembly (Westchester Co.), serving in the
37th New York State Legislature. ==Personal life==