Yorktown found two more slave ships, the Pons on September 30th, 1845 near Kabenda and the Panther on December 15th, 1845 also by Kabenda. Both ships were confiscated and their human cargo released. Yorktown continued to cruise the African coast until May of 1846 when she was recalled to the United States, sailing into Boston on May 29th. Again she needed repairs and was decommissioned on June 9th, 1846. She remained in reserve for some 29 months before she was recommissioned at Boston Harbor, supplied and crewed for her second mission with the African Squadron. She left Boston waters on November 22nd, 1848. Her mission saw her continuing to inspect ships while on patrol along the east coast of Africa. However, this tour provided no luck in finding slave ships.
On September 6th, 1850, USS Yorktown was sailing in unfamiliar waters of the Cape Verde Island group when she struck a hidden reef about a mile offshore of Maio Island. The keel of the Yorktown broke causing massive damage and as she pivoted on the reef before breaking up and sinking. Luckily all of her hands were able to make it ashore with absolutely no loss of life. Her captain, Commander William Harwar Parker, kept his men together on Maio Island for 32 tranquil days under the sun waiting for rescue when, on October 8th, her sister ship - the USS Dale - arrived at the island. The USS Dale picked up Captain Parker and crew and, within days, all were transferred to the USS Portsmouth who was enlisted to sail them to home port at Norfolk, Virginia. The crew of the stricken USS Yorktown were pleased with their successful mission that freed some 1,000 Africans from a life of bondage. Away from home for two years they arrived in Norfolk in early December of 1850, USS Yorktown crewmembers were paid their earnings and sent home for Christmas before being reassigned to a new ship.