In 2261, he joined the Resistance during the Earth Alliance Civil War. He was the commanding officer of the EAS Agamemnon, though he relinquished command to Captain John Sheridan, the ship's former CO, during the Battle of Mars. Sheridan expressed trust and affection for Captain James, whom he had trained and mentored. During subsequent battles, he functioned as executive officer to Sheridan as well as liaison to the fleet. Prior to Sheridan's assignment to Babylon 5 in 2259, he also served as the captain's XO.