For most history buffs, the Civil War’s sesquicentennial ends on Thursday. That day in 1865, Confederate Gen. Robert E. Lee surrendered to Ulysses S. Grant at the Battle of Appomattox. Most historians, though, acknowledge that the war’s most ambitious aim—full equality for black citizens—took many more years to accomplish, and even continues. But in his new book, After Appomattox, historian Gregory P. Downs makes a far bolder claim. Appomattox hardly ended the war: A full-scale military occupation continued for at least another five years, and without it, slavery may have persisted far longer than it did. Almost 100,000 Army soldiers remained in the South through the end of 1865, Downs meticulously documents, with up to 20,000 troops stationed there until 1871.

For decades, historians have brushed off this military presence as meaningless—by comparison, 1 million Union soldiers were in the South just before Lee’s surrender. But in After Appomattox, Downs makes the case that the final end to slavery, and the establishment of basic civil and voting rights for all Americans, was “born in the face of bayonets.” Put simply, the military occupation created democracy as we know it. Downs’ book couldn’t come at a more opportune time, as American forces once again face the difficult question of how long, and to what ends, an occupying army must stay in conquered territory. After more than a decade of fighting abroad, we may be too war-weary to see that military occupations are sometimes a good, even necessary thing.

Downs begins his account by pointing out that even after the Confederacy surrendered, slavery was not yet legally abolished. Congress may have passed the 13thAmendment, which ended slavery, in January of 1865, but to become law three-fourths of state governments needed to approve it. The surprising hero here is President Andrew Johnson, who assumed office after Lincoln’s assassination on April 14. Though Johnson’s administration would quickly turn out to be a disaster for black civil rights, he played a critical role in ending slavery. Johnson claimed that as president, he had sole authority to end the war and would do so only if Southern states ratified the amendment. It was not an empty threat, thanks to those 100,000 federal troops instituting martial law in the South.

Johnson’s strategy worked: Seven of the 11 former Confederate states ratified the amendment by December of 1865. Yet the immediate aftermath also revealed just how tenaciously white Southerners held onto racial domination. Almost as soon as the occupying forces left, the states that formally abolished slavery began enacting Black Codes that made a mockery of freedom. Local Southern lawmakers denied blacks the right to testify in court, to vote, to own property, to move about freely without arrest....