Nobile returned to Rome in May 1942 and her family severed communication with Speier after learning of her Catholic baptism, effectively ending her reasons for emigration. During the German occupation of Rome 1943/1944 Pope Pius XII made arrangements for Giulio Belvederi, nephew of the former Pontifical Master of Ceremonies Pietro Respighi, to hide Speier in the Catacombs of St. Priscilla, under the nunnery. Hiding in the catacombs saved Speier from the Raid of the Ghetto of Rome on 16 October 1943 in which more than 1,000 Jews were deported to Auschwitz and all save 16 were killed. During this part of the war, the Museum was closed, until the end of September 1944, and many artworks from war-torn areas were shipped to the Vatican for storage. When it reopened, she continued with her work creating a detailed monuments inventory of the Vatican holdings, which resulted in several important finds. In 1946, in an antiquities storage facility, she found a horse head sculpted by Phidias which was originally from one of the pediments of the Parthenon. On further examination, it was established from its weathering that it was in fact the second horse of Athena's chariot on the western gable, where the dispute between Athena and Poseidon over the land of Attica is depicted. Speier also discovered the two so-called ancient Aurai statues that decorated the exterior of the Sala Rotonda when it was built in the 18th century. She published "Die Skulpturen des Vaticanischen Museums" (The Sculptures of the Vatican Museums) in 1956 about the find of the Parthenon horse's head, and earlier in 1950 had published a distinguished report concerning the excavations of St. Peter's Basilica in Herbig's "Vermächtnis der Antiken Kunst" (Legacy of Ancient Art) entitled "Die neuen Ausgrabungen unter der Peterskirche in Rom".