Following consultation with his local bishop Victor Reed, Rother attended Mount Saint Mary's Seminary in Emmitsburg, Maryland from which he graduated in 1963. Bishop Reed ordained him to the priesthood on May 25, 1963. Rother served as an associate pastor in various parishes around Oklahoma: Saint William in Durant, Saint Francis Xavier and the Holy Family Cathedral in Tulsa, and Corpus Christi in Oklahoma City. In 1968 – at his request – he was assigned to the mission of the archdiocese to the Tz'utujil people (also spelled Tz'utuhil) located in Santiago Atitlán in the rural highlands of southwest Guatemala. While he was at Corpus Christi, he had learned a priest was needed in Guatemala and so applied and was accepted by Reed in 1968.