A lot of ground’s been covered here, but the bottom line is that Peter is under the Basilica San Pietro in Rome. The most obvious problem with the Jerusalem story is the claim that Peter was found in a Christian cemetery. In the first century, with Christianity an outlaw religion, there simply were no Christian cemetaries. That’s why early Christians were buried in the catacombs or common cemeteries. In these cemeteries of the 1st century we find various pagan religions, Christians, Jews, etc. There were no exclusively Christian cemeteries at that time anywhere in the Roman Empire of which Jerusalem was a part.
St Peter’s is the 2nd basilica on the Vatican Hill, the first having been built by Constantine in the 4th century. In order to construct it the Emperor had to level the cemetery and haul thousands of tons of dirt, removing it from the higher portion of the hill and filling in the lower portion. This was a monumental undertaking, not to mention a sacriledge for the dead buried there. Why would Constantine go through this kind of trouble, risking political damage and making his task so onerous? Because Tradition told him Peter was buried on the Vatican Hill. Pilgrims visited the site for over 3 centuries to see the tomb of the Apostle. It was well known in the Christian community where Peter was buried. It was also well known that he was martyred in Nero’s circus nearby, crucified upside down around 64-67 AD.
Constantine encased the tomb in a marble vault and built his basilica so the altar was placed directly above it. That basilica lasted centuries until it had to be rebuilt and replaced by the current basilica. When the new St Peter’s was built, the architects went to great care to place the present alter with it’s huge brass baldacino directly over the marble vault for the same reasons as Constantine: that Peter would lie beneath the altar.
Around the same time as the “discovery” of Peter in Jerusalem, the Vatican undertook excavations under the basilica to verify Peter’s presence. First they uncovered Constantine’s marble vault, carefull not to upset the footings of the basilica. Inside the vault they found a simple tomb, marked by a small altar like structure, very similar to the one described in the ancient histories. Next to the tomb was a large brick wall, soon to be known as the grafitti wall for all the ancient writing that was on it.
They found no bones in the tomb, but did find the bones of a man inside the wall! Among the inscriptions on the wall was one that read, “Here is Peter.” The bones had been hidden by ancient Christians concerned for their survival during the years of persecution.
The bones were assembled and tested. They were from a first century man of stocky build who was roughly in his 60s. They matched Peter. The Vatican doesn’t say with certainty that they are the saints remains. They refer to them as the bones that could be Peter. Still, when you see the ancient documentation, explore tradition and add up the unnecessary difficulties of placing the basilica where it was placed, you have to conclude that St Peter is most likely where the Church has always claimed.
I’ve seen the excavation and the tomb as well as the remains of the necropolis that once stood on the surface of the Vatican Hill. For my money, that’s where St Peter is buried.
Ancient historians describe Peter’s tomb and even made rough scetches of it for posterity.