He was sent to Rome to work at the Holy See as a private secretary of Cardinal Augustin Bea SJ from 1958 until 1964. This brought him into contact with Pope John XXIII. Martin's years in Rome coincided with the beginning of the Second Vatican Council (1962–65), which was to transform the Catholic Church in a way that the initially liberal Martin began to find distressing. He became friends with Monsignor George Gilmary Higgins and a fellow Jesuit priest, Father John Courtney Murray.