Twenty years later, in May of 1861, Cooke resigned his commission in the United States Navy to join the Confederate Navy.

    In the fall of 1861, Cooke was appointed official liaison between North Carolina contractors and the Confederate Navy Department.  Soon after, he was promoted to the rank of Commander.

    Cooke, was assigned responsibility of overseeing the building of three armored floating batteries, the CSS Albemarle at Edwards Ferry, the CSS Neuse at Whitehall (Seven Springs) on the Neuse River and an unnamed ironclad at Tarboro.

    In the capacity of overseer, Cooke found himself traveling around North Carolina coordinating the building of ironclads and attempting to locate boat-building materials including iron for plating the gunboats.

    Iron from the railroads became a primary source.  Cooke, for example, managed to secure through negotiations with the Atlantic and North Carolina Railroad Company the railroad tracks that ran between Kinston and New Bern.  These tracks had become of no use to the Confederates because New Bern had fallen into the hand of Union forces.

    North Carolina Governor Zebulon Vance agreed for the railroad iron to be taken and shipped to either Richmond, Virginia or Atlanta, Georgia to be rolled into plate under the stipulation that it be used for the defense of the state.  In particular, the governor noted that the railroad iron should be used on the ironclads being inland on the Neuse and the Roanoke.

    Propellers and propeller shafts for the ironclads were fabricated in the Confederate Navy yard at Charlotte.  Stem engines were obtained wherever they could be found.
Although no one knows for sure, some people claim the engine for the Albemarle was converted from "a large saw mill."

    The Neuse is said to have taken her boiler from a steam locomotive "probably" from the Baltimore and Ohio No. 34 and her engine from a saw mill in New Bern.

    In all, the construction of naval vessels in North Carolina, particularly inland on the Neuse and Roanoke Rivers, was greatly retarded by difficulty in obtaining iron for plating.  Both the Albemarle and the Neuse suffered long delays in construction because of the shortage.
 
    In the case of the CSS Neuse, these delays were fatal.  And although construction of the Neuse had begun at the same time as the Albemarle, the shipbuilders at Whitehall on the Neuse River had to dodge Union troops who were constantly passing through the little town.