That opportunity finally arrived in October 1864 at sea in the central Atlantic, where he converted the English steamerSea King to the Confederate cruiserCSS Shenandoah. As her commanding officer, Commander Waddell made a long and productive cruise through the south Atlantic, across the Indian Ocean and into the north Pacific. In the Arctic waters there, he devastated the United States flagged whaling fleet during June 1865. However, by then the Civil War had been effectively over for more than two months and, when he received confirmation of this fact in early August, Waddell disarmed his ship and took her back to England.
Waddell did not return to the United States until 1875, when he became captain of the commercial steamer City of San Francisco. He later was in charge of the State of Maryland'soyster regulation force. James Iredell Waddell died at Annapolis, Maryland, on March 15, 1886.