John J. Pettus, the governor who led Mississippi to secede in 1861 was term-limited and could not run for reelection. Clark ran for governor in the
October 1863 election on a conservative platform focused on caring for wounded soldiers and their families, as opposed to the "
fire-eater" rhetoric that had led to secession after Pettus's election. Clark was elected as governor with 70% of the vote and inaugurated at
Columbus on November 16. Clark's administration focused on aiding the destitute civilian population of Mississippi, officially sanctioning contraband trade with US forces in exchange for essential goods and medicine. By the time Clark came into office, Mississippi could contribute very little to the Confederate war effort. The major strategic points were already in Union hands, and Mississippi's army regiments were away fighting in other states. As Confederate demands for manpower increased, Clark sought to maintain a local military force under his control to oppose Federal raids and maintain law and order in the face of gangs of
deserters and
Unionist guerillas that had effectively overthrown civil authority in several Mississippi counties. Clark argued that as governor he had the authority to enroll men into the
Mississippi State Troops and exempt such men from
conscription, while the Confederate government sought to draft as many of his state troops as possible and complained that the state's armed force had "no discipline and order" and were "little better than an armed mob". Despite these conflicts over manpower, Clark coordinated the actions of his state troops with General
Nathan Bedford Forrest's
Cavalry Corps, the last remaining considerable Confederate force based in the region. In the final days of the war, Clark and former governor of Tennessee
Isham G. Harris proposed to General Forrest that they stage a fighting retreat into Texas and continue the war from there, which Forrest rejected. With the collapse of the Confederacy in the spring of 1865, Clark was forcibly removed from office by the
United States Army on May 22 and briefly imprisoned at
Fort Pulaski near
Savannah, Georgia. Clark was replaced as governor by
William L. Sharkey, a respected judge and staunch Unionist, who had been in total opposition to
secession. Clarke was ex officio President of the University of Mississippi Board of Trustees during his tenure as Governor of Mississippi. Despite losing the governorship, he remained on the Board for almost ten years after his term ended. In 1871, he purchased
Routhland, an Antebellum mansion in
Natchez, Mississippi. ==Death==