President Andrew Johnson blocked Republican Reconstruction measures at every turn, campaigned against the 14th Amendment and accused Republicans of "treason" for their attacks on him and their efforts to enfranchise blacks and "force" Republican principles on the South. Democrats rallied to Johnson's side, and Johnson and his supporters claimed the "Union" label in 1866 by forming the National Union Party. Johnson forced erstwhile "Union" Republicans to become more Republican. The issue shifted from "Union" to Reconstruction. Johnson took his case to the northern public in his "swing around the circle," but his coarse language and southern sympathies helped Republicans win huge majorities in Congress.

In 1867 the new Republican Congress passed the Reconstruction Acts, which divided the unreconstructed South into five military districts and extended federal oversight there. Johnson undercut congressional will by removing federal officers sympathetic to Republican Reconstruction. When Johnson fired Secretary of War Edward M. Stanton in 1868 for siding with Congress on Reconstruction, Republicans had enough. Congress impeached him for abuse of power. Johnson escaped conviction by one vote, but was chastened enough to end his obstructionism in his last few months in power.

Finally, Republican Reconstruction might be implemented. But establishing Republican governments in the South excited immediate and often violent resistance from conservative white southerners. The rise of terrorist organizations such as the Ku Klux Klan revealed the unpopularity and impotence of the Republican governments. Those governments begged for federal intervention, forcing Republicans in Washington to confront the Reconstruction issue again.