A military governor was appointed in each state by the President by virtue of his authority as commander in chief.
This official, aided by a civilian staff of his own choice and supported by the United States army and other Federal agencies, reorganized the state administration and after a few months turned the state and local governments over to regularly elected officials.

Restoration should now have been completed, but Congress refused to admit the senators and representatives of these states, and entered upon a fifteen months' struggle with the President over details of the methods of the reconstruction.

Meanwhile the Southern States, though unrepresented in Congress, continued their activities, with some interference from Federal authorities, until Congress in 1867 declared their governments nonexistent.
The work begun by Lincoln and Johnson deserved better success.

The original plan restored to political rights only a small number of Unionists, the lukewarm Confederates, and the unimportant.

But in spite of the threatening speeches of Johnson, he used his power of pardon until none except the most prominent leaders were excluded.