Much of eastern Tennessee remained in Confederate hands, and the ebb and flow of war during 1862 sometimes brought Confederate control again close to Nashville. However, the Confederates allowed his wife and family to pass through the lines to join him.[94][95] Johnson undertook the defense of Nashville as well as he could, though the city was continually harassed by cavalry raids led by General Nathan Bedford Forrest. Relief from Union regulars did not come until General William S. Rosecrans defeated the Confederates at Murfreesboro in early 1863. Much of eastern Tennessee was captured later that year.[96]
When Lincoln issued the Emancipation Proclamation in January 1863, declaring freedom for all slaves in Confederate-held areas, he exempted Tennessee at Johnson's request. The proclamation increased the debate over what should become of the slaves after the war, as not all Unionists supported abolition. Johnson finally decided that slavery had to end. He wrote, "If the institution of slavery ... seeks to overthrow it [the Government], then the Government has a clear right to destroy it".