For four decades, Shores was deeply involved in civil rights challenges, handling dozens of cases primarily for the Birmingham branch of the NAACP on behalf of African Americans. In the 1940s, the Birmingham NAACP grew to more than 8,500 members and received recognition from the national NAACP as its most outstanding branch for work combating police brutality, voting rights abuses, and employment discrimination, including unequal pay for Black public school teachers. The local branch raised $10,000 from area churches to challenge racial zoning in the courts, and Shores filed all of the legal challenges for Blacks who moved into the Dynamite Hill area. His affiliation with the NAACP led to a close friendship with Thurgood Marshall, who assisted Shores and Rev. Fred Shuttlesworth in the 1952 case of Autherine Lucy, who in 1956 became the first African American to integrate the University of Alabama in Tuscaloosa. Shores also helped Marshall and other NAACP lawyers in the 1954 Supreme Court case Brown v. Board of Education, which dismantled the racially motivated separate but equal doctrine. His profile rose even higher in June 1963 when he handled the case of Vivian Malone and James Hood, who gained admission into the University of Alabama despite Gov. George Wallace's stand in the schoolhouse door.