At age 28, Thomas Mellen, 2nd married 21 year old Catherine (Katie) Ingraham Courtney on August 20, 1862. She was the daughter of Dennis Courtney and Amanda Fisher of Edgartown.

Three months after the very successful voyage on the Onward the owners gave Thomas Mellen command of another of their vessels, the Levi Starbuck. The Starbuck left port on October 18, 1862 with great anticipation. Five days later and 500 miles from the Atlantic Coast, the mood turned sour. In the midst of the American Civil War, the Starbuck was captured by the Confederate Ship Alabama on Sunday, November 2.

When Captain Mellen was asked to lower the Levi Starbuck's flags by Captain Semmes, he refused, which resulted in the burning of his vessel and he was taken captive. Filled with fresh food and supplies for a 30 month voyage to the Pacific, the Starbuck was a prize for Captain Semmes and the crew of the Alabama.

After being held prisoner aboard the Alabama for 18 days, Mellen was freed in Fort DeFrance in Martinique in the West Indies. Once he connected with the American Consul there, he headed north aboard a French brig from St. Thomas to New York. Capt. Charles Seabury then offered him free passage from New York to New Bedford. Disappointed, but safe, he returned home in dismal financial shape because of the burning of the Levi Starbuck. However, a second voyage aboard the Onward would enable him to recoup much of those losses.

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