The first obstacle that Reconstruction faced was the very president who started it, Andrew Johnson. Johnson became president following the assassination of Abraham Lincoln in May of 1865. Johnson announced a new plan for Reconstruction, canceling out Lincoln's plan, within a month of the assassination, and without consulting Congress. (Boyer, et al., The Enduring Vision, 574) This action marked the beginning of a conflict between the president and Congress, Radical Republicans in particular. The conflict eventually resulted in increased difficulties for Reconstruction. Johnson's Reconstruction led to the pardoning of approximately 13,000 former Confederates and wealthy Southerners. These groups helped write the so-called "Black Codes," a set of laws which left the freedmen some basic rights gained by the 13th Amendment but which essentially kept former slaves from being truly liberated. (Boyer, et al., 575-576)
Confronted with a president whose Reconstruction plans were viewed as feeble, moderate and radical republican factions joined forces. The new coalition worked together to overturn the black codes with Lyman Trumbull's Supplementary Freedmen's Bureau bill.