There are 3 levels to St. Peter's---the main basilica level, the 2nd level grottos, housing the papal tombs, and the 3rd level necropolis.
Tradition always held that the Basilica was built on the spot where Peter was buried---but that was not verified until the 20th century, when they started digging and discovered the necropolis (while digging the tomb for Pius XI). If you write to the Vatican Excavation Office (Ufficio Scavi) months ahead of your visit (and you must write ahead---you can't just walk up to the office and ask), you might be one of the lucky few who get to experience the Scavi Tour. We were lucky.
You have to go through a metal detector to get into any part of St. Peter's --- to get to the Ufficio Scavi you start with the police and the metal detector and then you proceed to where the Swiss Guards are. We arrived at 8:43 for our tour. The Swiss Guard told us that we could go in at.....8:45. They are, after all, Swiss.
They take only 150 people per day to the necropolis under the Basilica---we were lucky enough to have an excellent guide who is also an archaeologist. And so we walked the streets of the 1st century city of the dead--and had the opportunity to see and pray at the tomb of St. Peter. It is, as tradition always said, directly under the papal altar. Science (and archaeology) proved the tradition!
No photos allowed during the Scavi Tour, but you can take the tour on Google street view---seriously!
The tour ends in the grottos---again, no photos allowed there either. And then, you can go back into the Basilica without having to go through the metal detector again.
This time, St. Peter's was full of tourists, tour guides, and general chaos. The only quiet oasis is the Blessed Sacrament chapel, where we stopped to pray.
Then a quick walk around the church and out and away from the chaos......
But I think that every Catholic should step inside of St. Peter's, at least once in life. Breathtakingly magnificent. I think that even people who are not Catholic, feel Catholic in St Peter's.....
1. St Peter's!
2. Tomb of Pope John Paul II
3. Tomb of Pope John XXIII
4. St. Peter's Square
5. Excavations Office
6. Workers and nuns in the collonnade near the Bronze Doors---I thought this was funny!