My Mystics, Saints, and Sinners class went to the Vatican to see the Scavi tour, which tours underneath St. Peter's Basillica. Before St. Peter's was built, there was a pagan cemetery which was later taken over by Christians. Also underground is the Necropolis, or the site of St. Peter's bones. The bones are inside the wall of this underground temple thing. The wall in which the bones were buried had a lot of Christian graffitti on it so scientists could interpret the meaning of that space. Two other sets of bones were discovered before St. Peter's but neither skeleton except his fit the description: 67, robust frame, and no feet (since he was crucified upside down, his feet were cut off).
One bishop in charge of the excavation was concerned about respecting the burials of the bones so when bones were found he had them packed up so they could be buried in a consecrated space at another time. He accidentally packed up the bones of St. Peter but fortunately they were found and now rest underneath St. Peter's.