Nile recommissioned in March 1858 under the command of Captain Henry Ducie Chads. When he was promoted to Vice Admiral, Nile became his flagship based at Queenstown in County Cork, Ireland. After exercising with the Channel Fleet during the summer, Nile departed for the North America and West Indies Station in October, but was caught in a hurricane and returned to Cork for repairs some forty days later. After further repairs at Plymouth, she finally started out for the Royal Naval Dockyard in the Imperial fortress colony of Bermuda (located in the North Atlantic, and administratively part of British North America, Bermuda was the headquarters and main base of the station) in April 1859 under the command of Captain Edward King Barnard and carrying the flag of Rear Admiral Alexander Milne, the Commander-in-Chief, North America and West Indies Station. Nile operated from Bermuda and Halifax during the tense period following the Trent Affair, when the United Kingdom's entry into the American Civil War seemed possible, eventually cementing cordial relations with the Union by means of a visit to New York City in September 1863. Returning to Plymouth in the following April, she was decommissioned and returned to the reserve, where her engines, boilers and propellers were removed.
