It's real name is the tour of the Vatican Necropolis. "Scavi" is just the Italian word for "excavation", and I don't know why people call this the "scavi tour". Once on this forum, someone asked about the scavi tour, and a Roman asked "Which scavi?" Rome is full of "scavi". Even the excavations for the construction of a building are called scavi.
The Necropolis tour takes you to the excavations of an ancient Roman cemetery under St. Peter's Basilica. For centuries it was reported that the main altar of St. Peter's Basilica was constructed over the main altar of the earlier basilica, which was constructed right over the tomb of St. Peter. In the 20th century, excavations were started to find the tomb. I once was told by a guide on this tour that when the cemetery was first found, the clergy were shocked to find a pagan cemetery, so they stopped the work and didn't resume it until a later time. This sounds fishy, because even an untutored lay person should realize that when St. Peter was crucified, all the cemeteries in Rome were pagan cemeteries. I've also read that the excavations were stopped because of World War II, which sounds more plausible. In any case, eventually they found what seemed to be the tomb of St. Peter, with an insciption identifying it, but it was empty. However, a short distance away, and higher up, they found the remains of a middle aged man from the same period. It's now believed this is the body of St. Peter. During one of the imperial persecutuions, the body was moved for safekeeping, probably to the catacomb of San Sebastiano, and brought back at a later date. When the Emperor Constantine built the first basilica, he leveled the ground, chopping off the tops of the tombs that were too high, and filling in the low spots with rubble. The tomb may have been moved a little higher to keep it from being buried. In very early times, a small chapel had been built above the tomb, where pilgrims came to pray. When the first Basilica was built, the Chapel of the Confession was built around this original little chapel.
When you take the tour, you're taken along an ancient Roman road, and shown some painted pagan and Christian tombs. Finally you see the supposed tomb of St. Peter, and then you're taken up into the crypt of the basilica, to the Chapel of the Confession, where you can look down a little opening and see a lamp that supposedly burns before the actual body of St. Peter.
If you don't take the tour of the Necropolis, you can enter the crypt from the main floor of the basilica, by a stairway near the main altar. There's no charge to enter the crypt. Here you can see the Chapel of the Confession, with the niche that is above the tomb. You usually can't enter the chapel, but it's open at the front and you can kneel in front of it. You can see the tombs of many other popes in the crypt.
If you do take the tour, after it's over, you can visit the crypt and then go up to the main floor of the basilica and so visit the basilica without having to wait in the sometimes-long security queue. (You'll have gone through security already before taking the necropolis tour.)
The tour is interesting, but I don't think it's something you should ruin your schedule for. You can see as much of the tomb from the crypt as you can from the excavations below. If you want to see painted Roman tombs or an ancient Roman street, there are other places in Rome to see those.