The Catacombs of St. Lucy are one of the oldest and most important monuments among the Christian communities of Siracusa and Sicily in the late Roman period. The name of the complex derives from a tradition, according to which Saint Lucy was buried here, after her martyrdom in the early 4th century AD, under the reign of Diocletian. A large underground cemetery extends beneath the homonymous square. The cemetery gradually grown from the 3rd to 5th AD, as it incorporated pre-existing constructions once used for funerary, religious and industrial purposes, by transforming them into monumental burial chambers. One of the most significant structures is the so-called “Pagan Shrine”: a chamber that dates between the 1st BC and 1st AD, prior to the foundation of the cemetery and frescoed with mundane themes and pagan deities. The Shrine is located in the South-West corner of Regio C, that is a hard and rather dangerous area to reach, never opened to the public and visited only by few scholars over the past decades.The excavation project undertaken in the years 2011-2015 by the Pontifical Commission of Sacred Archaeology, in association with the Arcadia University and the University of Catania, led to the development of the first virtual replica of the Shrine, using the Image Based 3D Modeling technology processed via Agiosoft Photoscan on the workstation of the Arcadia Virtual Archaeology Lab. This new approach facilitated an accurate examination of both structure and its decoration, allowing us to propose now a new theory about the original purpose of the room, traditionally regarded by scholars as a place for worshipping Zeus Peloros.