On May 5, 1803, Somers was ordered to Baltimore, Maryland, to man, fit out, and command Nautilus, and when that schooner was ready for sea, to sail her to the Mediterranean. Nautilus got underway on June 30, reached Gibraltar on July 27; and sailed four days later to Spain. He then returned to Gibraltar to meet Commodore Edward Preble, in Constitution, who was bringing a new squadron for action against the Barbary pirates[?]. Nautilus sailed with Preble on October 6 to Tangier[?] where the display of American naval strength induced the Europeans of Morocco to renew the treaty of 1786. Thereafter, Tripoli became the focus of Preble's attention.
Somers' service as commanding officer of Nautilus during operations against Tripoli won him promotion to master commandant on May 18, 1804. In the summer, he commanded a division of gunboats during five attacks on Tripoli.
On September 4, 1804, Somers assumed command of bomb ketch Intrepid which had been fitted out as a "floating volcano" to be sailed into Tripoli harbor and blown up in the midst of the corsair fleet close under the walls of the city. That night, she got underway into the harbor, but she exploded prematurely, killing Somers and his entire crew of volunteers.
Several ships of the United States Navy have been named USS Somers in his honor.
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