Served as captain of the 9th Maine Volunteers in 1861, then as Major Lt. Colonel and Colonel from 1862-1864. Under General Truman Seymour, Emery and the 9th Maine Volunteers were ordered to capture Morris Island and parts of James Island in an attempt to gain control of the area around Charleston Harbor, South Carolina. With control of these islands, the Union army could bombard Fort Sumter, which was preventing the Union Navy from entering the harbor. Surrounded by beaches and marshes and containing a 1,700 man garrison, 12 cannons, and a 10-inch "Columbiad" that fired 128-pound shells, Fort Wagner on James Island made it difficult for an attack using infantry. However, Seymour attempted to seize the island twice, and Sabine Emery was wounded during the first attack.