Fee spent most of the Civil War years in exile in Ohio, preaching and raising money for Berea College. Visits to Kentucky usually culminated in mob attacks, and an attempted return in 1862 ended abruptly with the Confederate invasion of Kentucky. In April 1864 Fee was able to return to Berea and resume his work. In July he moved to nearby Camp Nelson, Kentucky's black-troop recruiting center, where he established schools and held religious services for recruits and their refugee families.
By the close of the Civil War, Fee's ideas had reached their fruition. More than any other American of his day, he understood the racial problems facing America and proposed solutions that would have ameliorated much of the strife that later complicated race relations. Realizing that a landless, uneducated people newly freed from slavery required assistance, Fee implored the Federal government and northern businesses to assist blacks in acquiring jobs, land, and an education. Fee's Berea, a classless, integrated, nonsectarian Christian community where black and white landowners lived, worked, and shared the benefits of education at Berea College, served as an example of "the brotherhood of man." …Mercifully, Fee did not live to witness the demise of his dream. Three years after his death, when blacks comprised only 16 percent of the student body, Kentucky passed the infamous Day Law, which ended racial integration at Berea until 1950.