Comber attended all four sessions of the Second Vatican Council. After the Council he was appointed as a member of the Post-Conciliar Commission on Missions. After his term as Superior General he served as an Auxiliary Bishop in the Archdiocese of New York. Cardinal Spellman appointed him the pastor of the Church of the Transfiguration in Lower Manhattan in 1967. He retired after two years and moved to the Maryknoll Development House on East 39th Street. Later that year he moved to St. Agnes Rectory in Midtown Manhattan. He served as auxiliary bishop until his resignation was accepted by Pope Paul VI on January 12, 1976. As his health declined Comber moved to the St. Teresa Residence in Ossining where he remained until his death. He died on March 27, 1998 at the age of 92. His funeral Mass was celebrated in the Queen of Apostles Chapel on April 1, 1998 by New York Auxiliary Bishop Patrick Sheridan. He was buried in the Maryknoll Center Cemetery.