President Andrew Johnson's Reconstruction policies differed radically from President Lincoln's because:

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Andrew Johnson's Reconstruction policies differed radically from Abraham Lincoln's largely because Johnson was a Southerner who was sympathetic to the former Confederacy and wanted to leave the Southern states in charge of their own governments. He never supported the Confederacy, but once the war was over, he favored allowing them to re-establish their own state governments without federal influence. Doing so would have resulted in the states adopting many of the same policies that they had in place before the war, subsequently dooming the freedmen to lifestyles that were really no better than enslavement.
Lincoln and other progressive Unionists believed that federal intervention was necessary to effect a social coming of age in the region, which would have helped ensure the freedmen's rights and safety more effectively than Johnson's policies. Lincoln and Johnson only ended up on the presidential ticket together in 1864 (during Lincoln's re-election campaign) because Johnson was the only Southern senator who did not leave the federal government to join the Confederacy during the war. He was chosen to replace Lincoln's original vice president, Hannibal Hamlin, because the Republicans believed that adding Johnson to the ticket would encourage loyal citizens residing in the South to support Lincoln's campaign. Once he was president, Johnson also attempted to expedite Reconstruction and end it in 1865, when virtually nothing had been accomplished to ensure racial equality or rebuild the South.

President Andrew Johnson's Reconstruction Policies Differed Radically from President Lincoln's