The USS AIligator's keel was laid 26 June 1820 and was launched 2 November 1820 by the Boston Navy Yard and commissioned in March 1821. She had a brief but remarkable career. Designed by William Doughty was the last of the five 12-gun schooners specifically built to combat and stop pirates and slave traders. Master Commandant R.F. Stockton was placed in command and she set sail for the west coast of Africa with Dr. Eli Ayres on board on 3 April. The two were on a mission. Previously, the American Colonization Society (ACS) had been established in December 1816 in Washington, D.C. It sought the return of African Negroes to Africa. Among its members was Henry Clay, Daniel Webster, Thomas Jefferson, John Randolph and other eminent statesmen. Dr. Eli Ayres of the Alligator was to select and acquire territory to colonize free men of color in their native continent.

       At Cape Mensuado Stockton and Ayres met the local chiefton, King Peter, and a suitable tract of land was purchased by bartering. This land became the Republic of Liberia.

       The Alligator returned to Boston in July and again set out for Africa on 4 October 1821. The Alligator engaged a Portuguese pirate ship, the Marianna Flora, overcame her crew, captured her and placed a crew aboard her to be taken to the United States. The Alligator continued her cruise and captured several other slavers before returning to Boston. Stockton, California is named after him.

       In June of 1822 she was assigned to hunt pirates in the West Indies under the command of Lt. William H. Allen.

       In November, 1822, while the U. S. schooner Alligator was at anchor in the harbor of Matanzas on Cuba's northern coast. Lt. Allen was informed by two Americans that their ships, an American brig, Anna Maria, and schooner had been captured recently, were lying in a bay 42 miles to the eastward at Guajaba and being held for $7,000 ransom which they were to bring back. Instead, the two were outfitting a small schooner, the Ploughboy, in effort to recover their ships.

      The Alligator, its small cutter and the Ploughboy got under way and the next morning at daylight anchored near the bay. What they found was a nest of captured American ships. They could see an American brig, schooner, with three other vessels at anchor in the harbor. In amongst them was a pirate schooner under sail and full of men, with boats passing between her and the other vessels.

       The Alligator drew about 11-foot of water so being in familiar waters she lowered her armed boats. Lt. Allen, Captain Freeman with 12 marines prepared for attack. The second-in-command, Lt. John M. Dale and I I men took the cutter. The Captain of the Ploughboy and four men even took the Alligator's gig. The wind being light, the pirate schooner's crew tried to escape with sweeps [long oars]. After a long chase, the boats came within gunshot. The pirate schooner, identified as the Revenge, hoisted a red flag and opened fire; the boats prepared to board. A second pirate schooner then appeared and opened fire on Allen's boats. The pirates in the Revenge left her in boats, attempting to get aboard the other schooner. The Alligator's force then tried to head off the pirate boats, but they returned to the Revenge. The Americans made another attempt to board the vessel, but her crew again took to their boats and this time successfully got aboard the other pirate schooner. The pirates were joined by a third pirate schooner and escaped. The Americans then took possession of the Revenge while the boats unsuccessfully chased the other schooners.

       All this lasted only about half an hour and Lt. Allen was wounded twice. The combined pirate crews on board her numbered about one hundred. The Americans lost two, one being Lt. Allen, and five wounded. It was learned later that their loss was fourteen killed and a great number wounded. The Americans brought away their prize, the Revenge; also the American ship, two brigs, one was the Anna Maria, and two schooners.

      Command of the Alligator passed to Lt. Dale. Later. Commodore David Porter named the port at Key West "Allenton" in remembrance of Lt. Allen.

       They knew they were to sail through pirate infested waters and it was rumored that pirates would follow to capture any vessel that fell behind so they were to sail in convoy. On the 18th of November the Alligator got underway from Matanzas, Cuba for Norfolk, Virginia. One of those returning was the brig Anna Maria under Captain Somers. A brig is a two-masted square rigged ship and not as fast as the topsail schooner Alligator. The course was about north which would take them into the Gulf Stream and northward to Norfolk. Sure enough as the day wore on the Anna Maria and others fell behind and during the night Lt. Dale turned back and forth to slow her forward speed.

       As morning broke on November 19th only two ships of the convoy could be seen. By four in the afternoon only the Anna Maria was in sight and she was far to the west or closer to the reef. Preparing for the night they ordered extra precautions to remain in the Gulf Stream to avoid the reef to the west. At 9 p.m. the leadsman found no bottom at 270 feet of water, indicating deep water. Thirty minutes later the Alligator at about five knots per hour suddenly grounded herself on the Florida Keys reef.

       Lt. Dale quickly surveyed for damage and the Alligator was basically in good shape. Dale decided to take an anchor by boat off the stern and using the Alligator's capstan drag her off the reef. The anchor line broke and she remained hard and fast grounded. The crew began lightening the ship by throwing heavy items over board, but the wind shifted to the southeast and blew her farther upon the reef.

       At daybreak, of November 20 they hauled a larger anchor into deep water and heaved-to on the capstan. The anchor would not catch bottom and they simply reeled in the anchor. Time after time they failed. At the next high tide, Lt. Dale raised the sails and tried to drive her across the reef to the other side, but she remained grounded - so another night on the reef being slowly broken apart.

       On the morning of 21 November a Bahamian wrecking schooner arrived and Lt. Dale began transferring valuable items to her. In the meantime another sail appeared and by luck it was the brig Anna Maria. Now the wrecker was not needed and important items were transferred to the Anna Maria during the day.

       Darkness came and still another night aboard the floundering Alligator. On the morning of the third day, 22 November, Lt. Dale made a ship's captains choice - the ship could not be saved. The crew was sent to the Anna Maria and the young valiant and battle tested Alligator set afire to prevent her from falling into the hands of pirates. She soon blew up and saying farewell they set sail in the Anna Maria for Norfolk

       The Norfolk newspaper The American Beacon on December 4, 1822 reported, "Tuesday, Dec. 3. -The brigantine Ann Maria, Somers, of New York, from Matanzas, with sugar and molasses, having on board the officers and crew of the US schr. Alligator, which was totally lost on the 19th Nov. of Carysfort, on her passage to this port."

       A Court of Inquiry convened aboard the US Frigate Guerriere on December 13, 1822 exonerated the crew of the Alligator of negligence.