The Southern organizations had lost many ministers and many of their members, and frequently their buildings were used as hospitals or had been destroyed.

Their administration was disorganized and their treasuries were empty.

The Unionists, scattered here and there but numerous in the mountain districts, no longer wished to attend the Southern churches.
The military censorship in church matters, which continued for a year in some districts, was irritating, especially in the Border States and in the Union districts where Northern preachers installed by the army were endeavoring to remain against the will of the people.

Mobs sometimes drove them out; others were left to preach to empty houses or to a few Unionists and officers, while the congregation withdrew to build a new church.

The problems of Negro membership in the white churches and of the future relations of the Northern and Southern denominations were pressing for settlement.
All Northern organizations acted in 1865 upon the assumption that a reunion of the churches must take place and that the divisions existing before the war should not be continued, since slavery, the cause of the division, had been destroyed.