The reason why President Andrew Johnson was hit with a charge of breaking the Tenure of Office Act was that he tried to remove Edwin Stanton as Secretary of War.
President Andrew Johnson would often clash with the Radical Republicans who controlled Congress when it came to issues relating to the treatment of the South after the Civil War.
Andrew Johnson then tried to remove Edwin Stanton, who was the Secretary of War, because Stanton was pro-Republican. This led to Johnson being impeached for violating the Tenure of Office Act which said that some office-holders could not be removed unless approved by the Senate.
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