Basilica of San Clemente

Three layers of history stacked on top of each other, literally. The current 12th-century basilica sits on top of a 4th-century church, which sits on top of a 1st-century Roman house and a Mithraic temple. You descend through each layer, and by the time you reach the bottom you can hear an underground river running through Roman brickwork. The 12th-century apse mosaic upstairs is one of the finest in Rome. Entry to the lower levels costs €10 and is absolutely worth it. This is the single best way to understand Rome's layered history.