In December 1865, the Republican Congress rejected President Johnson's lenient plan for the reconstruction of the former Confederate states within the Union.  Over the next several months, Johnson vetoed Congressional legislation which sought to ensure the basic civil rights of black Americans.  In the Congressional elections of November 1866, Republicans won a majority large enough to override any presidential vetoes, and in 1867 began enacting their own Reconstruction program, which relied on enforcement by the federal army and federal courts.

Because of the military nature of Reconstruction, Secretary of War Edwin Stanton was at the center of the battle over it.  Stanton, a holdover from the Lincoln administration, initially backed the new president’s Reconstruction plan, but became distressed over reports of anti-black violence and resistance to federal control.  Stanton stayed in the cabinet to provide a voice for tougher Reconstruction policies, and worked behind the scenes with Congressional Republicans and General Grant, the commanding general of the army. 

In March 1867, Congress passed, over Johnson’s veto, the Tenure of Office Act which forbade a president from removing a Senate-confirmed appointee without the Senate’s express approval. The law was enacted in large part to protect Stanton.  When Stanton drafted Congress's third Reconstruction act, passed in July, President Johnson demanded his resignation.  After the secretary refused, President Johnson suspended him in August, while Congress was in recess, and named General Grant as acting secretary of war.  In January 1868, the reconvened Congress voted to reject Johnson's suspension of Stanton (here, the "Stanton Reinstated" dagger).  Grant promptly resigned as acting secretary of war, and Stanton resumed the position.

The federal courts were another avenue of Reconstruction controversy.  In November 1867, the editor of the Vicksburg (Mississippi) Times, William McCardle, was arrested by military officials for printing libelous editorials to incite rebellion.  Under the Reconstruction Acts, he was to be tried by a military commission.  To obtain release, McCardle appealed to the U.S. Supreme Court for a writ of habeas corpus.  Republicans feared that the Supreme Court might use the case to rule Congressional Reconstruction unconstitutional.  When Congress reconvened in December 1867, the Republican House passed a bill requiring a two-thirds majority of the Supreme Court to rule any Congressional act unconstitutional.  The bill (here, the "Supreme Court Bill" dagger) was eventually defeated in the Senate.  Congress did, though, restrict the Supreme Court's habeas corpus jurisdiction, making the McCardle case moot.