Searching for the CSS Alabama

This was not done, however, and Vanderbilt was turned over to the Union Navy on 24 March and fitted with a heavy battery of 15 guns at the New York Navy Yard during the summer of 1862. She left New York on 10 November and—after conducting a brief search for CSS Alabama, the most destructive Confederate commerce raider of the entire war—put into Hampton Roads, Virginia, on 17 January 1863.

Ten days later, Vanderbilt received orders to conduct a much longer and more thorough search for Alabama. This year-long cruise took the vessel to the West Indies, eastern coast of South America, Cape of Good Hope, St. Helena, Cape Verde, the Canary Islands, Spain and Portugal.

During the West Indies portion of her deployment, Vanderbilt served as flagship of Commodore Charles Wilkes' Flying Squadron. During the search, Vanderbilt captured the blockade-running British steamer Peterhoff on 25 February, off St. Thomas, Virgin Islands, causing a dispute between the British and Americans as to the disposition of mail carried aboard the steamer. President Abraham Lincoln eventually ordered the mail returned to the British.

Vanderbilt's captures also included the British blockade runner Gertrude, taken off Eleuthera Island in the Bahamas on 16 April, and the British bark Saxon, seized at Angra Peguena, Africa, on 30 October. Saxon was suspected of having rendezvoused with and taken cargo off CSS Tuscaloosa earlier. However, pursuing leads as to the whereabouts of Alabama, herself, became increasingly frustrating as Vanderbilt would often arrive at a port only to discover that her quarry had departed only a few hours earlier. She eventually returned to New York City in January 1864 for repairs without ever having sighted the Confederate vessel.

North Atlantic operations

Vanderbilt left New York City in September and cruised off Halifax, Nova Scotia, searching for blockade runners. The Halifax-Wilmington, North Carolina, route for blockade runners was used heavily at this time owing to outbreaks of yellow fever at Bermuda and Nassau, Bahamas. Nevertheless, the Union cruiser failed to take any prizes and put into Boston, Massachusetts, on 13 October.

She was deployed with the blockade off Wilmington in November and participated in the unsuccessful first amphibious assault upon Confederate Fort Fisher in the Cape Fear River, North Carolina, on 24 and 25 December. The Fleet took the fort during a second amphibious assault on 13 and 15 January 1865.

Vanderbilt returned to New York in late January, remaining until 24 March when she left for the Gulf of Mexico ferrying new recruits. From there, she proceeded to Charleston, South Carolina, towing the uncompleted Confederate ram Columbia from Charleston to Norfolk, Virginia, in May, and towed Onondaga from Norfolk to New York in June. Vanderbilt served as a receiving ship at the Portsmouth Navy Yard (Maine) during the summer of 1865.

Circumnavigating the Americas

USS Vanderbilt

The Civil War now over, Vanderbilt sailed from Portsmouth on 14 August and put into the Philadelphia Navy Yard on 27 August to be fitted put for a cruise around Cape Horn. She left Philadelphia, Pennsylvania, on 25 October and arrived in Hampton Roads three days later. There, she was designated flagship of a special squadron consisting of herself, Tuscarora, Powhatan, and Monadnock. The squadron was commanded by Commodore John Rodgers and intended to increase the Pacific Squadron to a 14-ship force.

The vessels left Hampton Roads on 2 November and arrived at San Francisco, California, on 21 June 1866 after stopping at most major South American ports while circumnavigating the South American continent.

Carrying Queen Emma to Hawaii

Vanderbilt was decommissioned at Mare Island, California, on 30 June, but was soon recommissioned and, on 13 October, sailed from San Francisco to Honolulu, Hawaii, with the Hawaiian monarch, Queen Emma of Hawaii, on board.