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He was present at the Battle of the Head of Passes of the Mississippi River on October 12, 1861, and at an engagement against Fort McRee near Pensacola, Florida, in November 1861.
Shortly after this incident, on January 10, 1861, the day Florida declared its secession from the Union, Slemmer destroyed over 20,000 pounds of gunpowder at Fort McRee, spiked the guns at Barrancas, and evacuated with 51 soldiers and 30 sailors to Fort Pickens.