If you ask Real Nice and far enough in advance when planning to visit the Vatican, you can get into the “Scavi Tour” where you get past the Swiss Guards and are admitted to the underground necropolis beneath the Vatican. Here you can see the 1st century graveyeard beneath the original St Peter’s beneath the current St Peter’s, where Peter was allegedly buried. At the end of the tour, after much build up, you are told that if you peep through a hole in the wall you’ll see where Peter’s bones were found. And you see a rock wall in the middle distance with a niche in it. And you get some BS story about how the bones COULD PROBABLY be St Peter’s according to non-transparent internal forensics conducted by the Church. They are CONSISTENT with St Peter. And those alleged bones of St Peter are not on display despite that they’re happy to have the mummified corpse of a couple of former popes on public display up above.
Yeah whatever. So that is what St Peter’s has buried under the main altar in the basilica. Fortunately the tour is cheap and has enough other points of interest to be arguably “worth it”.