Empire was chartered by the Virginia State Navy under Captain Milligan. She towed ballasted ships into position to assist in obstructing the channels of the river between the forts at Norfolk in May 1861. In that same month she twice sailed under a flag-of-truce with Capt. T. T. Hunter of the Virginia Navy to arrange with the Union commander off Fortress Monroe exchange of wounded Union prisoners and passage north from Norfolk of certain families wishing to return to their Northern friends. In the latter part of June 1861 she again served as the bearer of a flag-of-truce off Fortress Monroe, this time for Brigadier General Huger, CSA. In September 1861 Empire was to be provided with four guns transported by Superior and two rifled guns transported by Harmony to assist in a plan to drive Union forces from Roanoke Island. [See Appohattox, supra]
On 22 October 1861 Commodore W. F. Lynch, in his flagship Sea Bird off Roanoke Island, signed a contract with Gilbert Elliot, as agent for J. G. Martin, to build at Elizabeth City, N.C., a gunboat hull "to be fitted to machinery" out of steamer Empire. The engines were never transferred because the hull was not ready to receive them before Federal armies took the area. Empire, becoming Appomattox (q.v.), had further need of her power plant.