Remaining in port for six months while her masts and rigging were repaired, she finally sailed again on 26 July for the West Indies.[32] The Congress made routine patrols escorting American merchant ships and seeking out French ships to capture. On two occasions she almost ran aground; first, while pursuing a French privateer, she ran into shallow water where large rocks were seen near the surface.[26] Although their exact depth was not determined, Sever immediately abandoned pursuit of the privateer and changed course towards deeper waters.[33] Her second close call occurred off the coast of the Caicos Islands when, during the night, she drifted close to the reefs. At daybreak, her predicament was discovered by the lookouts.[34] On 29 August 1800, she recaptured the American merchant brig Experiment, which had been captured by the privateer Bayonnnese three days earlier.[35] On 2 October, she spotted the HMS Ticiphone with a brig following her, her prize [clarification needed]under tow. Sever decided to cut between the two ships and didn't notice there was a towline running between them until it was too late to avoid an accident. Sever sent an immediate letter of apology to Captain John Davie.[36]
A peace treaty with France was ratified on 3 February 1801 and the Congress returned to Boston by 3 April.[37][38] In accordance with an act of Congress passed on 3 March and signed by President John Adams, thirteen frigates then currently in service were to be retained. Seven of those frigates, including the Congress, were to be placed in ordinary (mothballedl.[39] On her way up the Potomac en route to the Washington Navy Yard, she passed Mount Vernon. Sever ordered her sails lowered, her flag lowered to half mast, and a 13-gun salute fired to honor the recently deceased George Washington.[40] After arriving in Washington, the Congress was decommissioned, along with the United States and the New York.[40][41][42]