Assigned to the llth district of the Mississippi Squadron, commanded by Lt. Moreau Forrest, General Thomas served as a patrol vessel on the Tennessee River, above Muscle Shoals. During this period Confederate General Hood was mounting his campaign into Tennessee to divert Sherman's march on Atlanta and General Thomas patrolled the river unceasingly to prevent the Southern troops from crossing. At Decatur, Ala., 28 October 1864, the gunboat engaged strong batteries from Hood's army. After passing the batteries downstream and sustaining several hits, General Thomas rounded to and, with Army gunboat Stone River, poured such a withering crossfire into the emplacements that the Confederates were forced to withdraw. After Hood's repulse at Nashville in December, General Thomas was used on the upper Tennessee River to block his escape route. She aided General Steed-man in his successful attack on Decatur 27 December by giving his army concentrated gunfire support, and attempted to pass over Elk River Shoals to prevent a Southern crossing of the river. The Tennessee was too low, however, and Forrest and his gunboats could not cross.

General Thomas returned to Bridgeport 30 December 1864, but was soon active again. On 26 February 1865 she joined the other gunboats of the llth district and, taking advantage of unusually high water, crossed Elk River Shoals. The ships destroyed the camp of Southern General Roddey, captured a quantity of supplies and destroyed communications at Lamb's Ferry before returning to Bridgeport 4 March. General Thomas continued to patrol between Bridgeport and Decatur, Ala., until she was turned over to the War Department at Bridgeport 3 June 1865.