In the summer of 1964, racial violence in the South escalated. The acts of violence included the firebombings of 44 black churches in Mississippi. As a result, the Sixth General Assembly of the National Council of Churches issued a "Call to Action on Race Relations." The American Friends Service Committee agreed to service teams of volunteers to help rebuild these churches. The Philadelphia Yearly Meeting responded to the National Council of Churches with a "Quaker Call to Action in Race Relations," which advocated that membership in Monthly Meetings be advertised as open to all races, housing, employment, and schools should be free of discrimination with regard to color, and that each individual should do his best to fight racial discrimination on every scale. It was also proposed that the Philadelphia Yearly Meeting should send a mission to Mississippi, to aid in the rebuilding of churches. New York Yearly Meeting was also interested in sending a mission of aid.

The "Mission to Mississippi," also called the "Mississippi Project on Church Reconstruction and Reconciliation", was a joint effort by the Philadelphia and New York Yearly Meetings to help rebuild the burned churches in Mississippi. George Corwin, clerk of New York Yearly Meeting, served as chair of the Joint Committee for Reconciliation and Church Reconstruction, which objectives were to rebuild the churches, and attempt to change the climate of racial interactions in the area by building a bridge between the black and white communities. The Committee sent Lawrence and Viola Scott to Jackson, Mississippi to serve as a "Quaker presence" there, and help to coordinate the rebuilding efforts. The project worked closely with the Committee of Concern, a Mississippi ecumenical group which raised $75,000 towards the rebuilding effort with a pamphlet entitled "Beauty for Ashes."

In 1965, Ross Flanagan reported to the New York Yearly Meeting that Friends had helped to reconstruct 33 of the 44 destroyed churches, with the help of the Pacific Yearly Meeting and the Mennonite Service Committee. In addition to rebuilding the churches, Philadelphia Yearly Meeting proposed that a community center, the "Madison County Freedom Center," should be built in the rural town of Canton, Mississippi. This was built in the summer of 1965. The Mennonites provided a couple to stay near the community center and foster its use and program, while Lawrence and Viola Scott lived in Jackson and taught in integrated schools, in order to foster racial harmony. The 1964 Philadelphia Yearly Meeting Committee on the Mississippi Project was laid down in 1966.