The war was fought over Southern independence, not over slavery. Lincoln said repeatedly the war was not being fought over slavery
. In August 1862, over a year after the war started, Lincoln wrote an open letter to a prominent Republican abolitionist, Horace Greeley, in which he said he did not agree with those who would only “save” the Union if they could destroy slavery at the same time. Lincoln added that if he could “save” the Union without freeing a single slave
, he would do so (Letter to Horace Greeley, August 22, 1862, published in the New York Tribune).
In July 1861, after the First Battle of Manassas (Bull Run) had been fought, the U.S. Congress passed a resolution, by an overwhelming majority, that declared the war was not being fought to disturb slavery, nor to subjugate the South, but only to “maintain the Union”
(i.e., to force the Southern states back into the Union). A few months later, in September, a group of Radicals visited Lincoln to urge him to make compulsory emancipation a war objective. Lincoln declined, telling the Radicals, “We didn’t go into the war to put down slavery, but to put the flag back” (Brodie, Thaddeus Stevens, p. 155; Klingaman, Abraham Lincoln and the Road to Emancipation, pp. 75-76). Later on, about halfway through the war, the Radicals and other Republicans succeeded in making the uncompensated abolition of Southern slavery a secondary goal of the war
. However, the primary purpose of the federal invasion was always to destroy Southern independence.