After Lincoln's assassination in 1865, two factions emerged on Reconstruction. President Andrew Johnson's conservative path put an emphasis on states' rights and returning land to the former slaveowners who had controlled it before the war. This path allowed the white elites in the South the opportunity to pass repressive "Black Codes" that all but re-enslaved the southern blacks.

The more progressive wing of the Republican party, called the Radical Reconstructionists, did not support strong states' rights for the South, instead advocating for federal control of the area. When the pendulum swung towards them, they divided the former rebel states into five federally administered military zones. The federal military presence in the South helped protect blacks from vigilante groups such as the Ku Klux Klan.

Opinion swung back and forth in the early post-war years between the conservative, states' rights approach to Reconstruction (which put power back in the hands of white plantation owners), and the progressive approach (that put increased power in the hands of blacks). Hampering progressive efforts was the prevalence of racism across the United States, leading to a backlash against racial integration.

Finally, in the what is called the "Compromise of 1876," Republican Rutherford Hayes made a deal with Democrats to allow them unfettered control of the Southern states. This was a decisive victory for a racist approach to structuring post-war Southern society, one that stayed in place until the emergence of the Civil Rights movement in the 1950s led to President Lyndon Johnson's signing of landmark Civil Rights legislation in the 1960s.

At first, Reconstruction was concerned with making sure that the political institutions of the South were changed to ensure that there would be no repeat of the secessionist uprising that had led to the outbreak of Civil War. To that end, it was important to protect the civil rights of the newly-freed slaves, to allow them to take their place in the new society as free citizens, voters, and office-holders.

White opinion in the South was generally hostile to any notion of civil rights for African Americans. That being so, Reconstruction necessitated the establishment of powerful federal agencies such as the Freedmen's Bureau, which provided food, medical aid, and legal assistance to former slaves in the South. Such concerted action at the federal level was necessary as the white supremacists still in control of the South's political institutions had no intention of protecting the civil rights of those they didn't believe should have such rights in the first place.

The fundamental weakness of Reconstruction was that it was wholly dependent for its success on sustained, concerted action at the federal level. Such action requires an extraordinary level of political will, the kind of will that is virtually impossible to sustain over any length of time. And so it proved with Reconstruction. Over time, policy-makers in Washington grew weary of the whole business of enforcing civil rights. Public opinion was also turning against the policy, feeling that it was a remnant of the Civil War from which most people wanted to move on. It became increasingly clear that there was nothing to be gained politically from maintaining the policy.

Added to that, most white people in the North were staunch white supremacists, no less than their Southern counterparts. Such Northerners may have believed in formal legal equality, but not in substantive equality between the races. So the impetus behind Reconstruction petered out. And without a sustained effort at the federal level to enforce civil rights, the Southern states gradually reasserted their control, erecting a legislative apparatus of racial discrimination—the notorious Jim Crow laws—which systematically stripped African Americans of their hard-won civil rights.