When Stefan Amaris' soldiers first secured control of Terra in 2770 and laid siege to the Vatican, Catholic Pope Clement XXVII dispatched a message to the five cardinals who oversaw the Church in the Star League's other Member-States. Correctly anticipating his death at the hands of the Greenhaven Gestapo, Clement stepped down from his position and granted the cardinals the temporary power necessary to run the church in their respective domains.
Clement intended for the College of Cardinals to elect his successor once the opportunity arose, but New Avalon's Cardinal Kinsey de Medici received a garbled message which he interpreted to mean that Clement had placed him in charge of the Church. Later, upon learning of the massacre of Clement and nearly everybody else in the Vatican, de Medici moved swiftly to assume control of the Church. Despite being informed of Clement's actual message, he appointed a new College of Cardinals who confirmed his election as Pope Thomas X, following which the new pontiff announced his authority over all Catholics in known space.
Cardinals and other Church leaders in the other states refused to recognize Thomas X's authority, prompting him to excommunicate them all. While the war against Amaris raged this split was more symbolic than practical, but following Terra's liberation in 2779 the College of Cardinals convened once more and elected John Paul V as Clement's successor. Thomas X's refusal to submit to him or step down prompted the official break between the Roman and New Avalon Catholic Churches.
Despite this split the Vatican didn't dispute the apostolic succession of the New Avalon Catholic Church, allowing them to continue to perform valid Sacraments.