After war,in 1863, President Abraham Lincoln designed a Reconstruction plan which aimed at reunifying the North with the South. His plan was based on the idea of forgiveness. Lincoln believed that the South should return to the Union.
This idea was in contrast to the Radical Republicans´ ideas. The Radical Republicans wanted to punish the South in some way therefore, they did not have the intention of reorganizing its society.
The U.S. military is subordinate to the Federal (civilian) government. Note that the US Congress controls the budget, and that the President is required to ask for a declaration of war, and the Congress then votes to approve or disapprove the request.