The war reversed the policy overnight. In September 1943 Stalin received three metropolitans in the Kremlin and permitted the election of a patriarch, the reopening of seminaries and the printing of a church journal, in exchange for the church's full support of the war effort; a Council for the Affairs of the Russian Orthodox Church was created to supervise the arrangement. Thousands of churches reopened, many of them in territory where the German occupation had already allowed it. The same period brought the forcible absorption of the Ukrainian Greek Catholic Church into Orthodoxy at a staged synod in 1946, and the deportation of its bishops.
The truce did not last. Khrushchev launched a renewed campaign from 1959, closing roughly half the parishes that had reopened, shutting most of the remaining monasteries and seminaries, and using tax, registration and the removal of parental rights rather than mass execution. Dissent went underground and abroad: samizdat appeals from priests and Baptists, the refusenik movement among Soviet Jews whose emigration became an international issue, and the persistence of Islamic practice outside the registered mosques.
The end came from within. The millennium of the baptism of Rus in 1988 was celebrated publicly with state approval, the law on freedom of conscience of 1990 restored legal personality to religious bodies, and after 1991 churches, mosques and synagogues reopened in numbers across every successor state.