The current Basilica of San Clemente in Rome dates to the 11th century, and was extensively restored and given a new facade in the 18th. In the 19th century it was believed that the current structure was the one records say was built in AD 392, but archaeology showed otherwise. When the site was excavated in the 1860s, it was discovered that this basilica was built above an earlier basilica, dating to the 4th century. That structure was built above earlier Roman remains. The bottom level seems to be some apartment blocks or insulae that were destroyed in the fire of AD 64. Then other houses were built. In the early fourth century a large house and some other buildings, possibly belonging to Titus Flavius Clemens, which was demolished to level the ground for the basilica.
You can visit these under-ruins, descending stairs past walls of different periods.
At the bottom you reach a well-preserved Mithraeum or Temple of Mithras, built in the basement of the Roman apartment block.
This chamber, the Triclinium or dining room, was used for ritual meals.
This room is the Scuola Mitriaca, where initiates learned the secrets of the cult.
As this plan shows, the Mithraeum -- the Triclinium is Q, the Scuola Mitriaca is R -- was part of a large complex of buildings. There may be an early Christian church at this level as well, although not all the sources mention it.