Religion did not start the Second World War, but every belligerent had to decide what to do with it. In Germany the National Socialist state promoted the German Christians, a movement that sought to purge Christianity of its Jewish inheritance, and was answered by the Confessing Church, whose Barmen Declaration of 1934 refused the state's claim over the gospel; its best remembered voice, Dietrich Bonhoeffer, was executed at Flossenburg in the war's final weeks. The Vatican's wartime course under Pius XII, a diplomacy of neutrality, quiet rescue and public restraint, remains the most argued question in the church history of the century, with the documentary record still being weighed.
The Soviet Union, which had spent two decades attempting to extinguish religion, reversed course under invasion: in 1943 Stalin received the surviving Orthodox metropolitans and allowed the reopening of churches and the election of a patriarch, purchasing wartime loyalty with a controlled revival that outlasted the war. In Japan, State Shinto supplied the war's sacral frame, from shrine rites for victory to the cult of the war dead at Yasukuni, and the Allied occupation's Shinto Directive of 1945 disestablished it, separating shrine and state for the first time in the modern era.
Across occupied Europe, clergy of every confession filled the camps alongside the communities they served: Polish Catholic priests died at Dachau in the thousands, and Orthodox, Protestant and Jewish religious life in the occupied East was targeted for destruction outright.
Sources The Second World War: A Complete HistoryMartin Gilbert with The Catholic Church and the Holocaust, 1930-1965Michael Phayer