The conflict between President Andrew Johnson and Congress after Lincoln's assassination primarily arose because Republicans disagreed with President Johnson's approach to Reconstruction. Johnson’s plan was seen as too lenient towards the Southern states that had seceded. While he aimed to quickly reintegrate the Southern states into the Union, many Congressional Republicans, particularly the Radical Republicans, felt that his policies did not sufficiently protect the rights of newly freed African Americans and did not adequately enforce civil rights.
Additionally, the Southern states began enacting black codes, which were laws designed to restrict the freedoms and rights of African Americans. These actions further inflamed tensions between Johnson and Congress, as they went against the Republicans' vision for Reconstruction, which included more protections for formerly enslaved people.
Therefore, the primary reason for the conflict was that Republicans disagreed with President Johnson's Reconstruction Plan, as it was viewed as too lenient and insufficient to address the needs and rights of the African American population.