A few weeks ago a friend of mine told me about the Vatican excavation tour. I went online and found the information on the Vatican website.
First, to take the excavation tour you must reserve in advance via email. You tell them you available date range and language you speak and they confirm your space (if available) via email. To increase your chance of getting a reservation, give them the widest date range possible. The confirmation does not come quickly and some have said they did not receive it until a few weeks before their trip. Once confirmed, you must pay €10 via credit card.
On the day of your tour you arrive 15 minutes before your scheduled time, go to the "holy gate" and tell the Swiss Guards you have an appointment at the excavation office. Once you arrive you pick up your ticket.
One note, they do not permit any backpacks or very large bags in the excavations. I did see 2 people being turned away. If you have these with you they can be checked at the coat check which is on the opposite side of St Peters. If you are late they wil not wait for you.
The tour of the excavation is amazing. The guides are very knowledgable and follow the entire tour through the history of St Peter and the building of the Vatican. Once you are lead underground the first area you see is the main street of the cemetary which was once located above ground. It was burried in order to build St Peters and only discovered in about 1935. Along the way you get to peek into a few of the masoleums along the main street of this pagan cemetary. In addition, your guide will also point out the signs and symbols of early Christianity. In one particular small tomb there are mosaics that are said to be the earliest Christian mosaic in the world. Towards the end of the tour you finally get to see the exact location of St Peters burial and the layers of monuments built around him. Each new monument to St Peter was built over and around the original one finally resulting in the great St Peters Basilica.
The tour takes about an hour and a half and for most of the time you are underground. The chamber of the site are artificially humidified to a level of about 90% to protect the environment. Try to wear lightweight clothing or you may find it uncomfortable.
Remember that only 100 people per day are allowed into the excavations, so if you get a confirmed reservation consider yourself honored. It's difficult to really explain what you will see, but it really is amazing.
Once I return home I will post the websight where you can make reservations.