It is said that, early in the first millennium, Peter, along with the apostle Paul, visited Rome to spread the faith of Christianity, when the Christians were often persecuted for their beliefs. Accordingly, the apostle Peter was also arrested and said to be crucified in an arena known as Caligula’s Circus in Rome in 64 AD, at the orders of the Emperor Nero. It is also said that Peter asked to be crucified on an inverted cross, as he felt he was not worthy enough to be crucified like Jesus. After his death, his body was taken outside the walls of the arena and there, on the side of what was called the Vatican Hill, he was buried, possibly in a small roofed grave.
Almost three hundred years later, Constantine, the first Christian emperor of Rome, started to construct a great church on the site of the tomb of St Peter which, by that time, had evolved from a simple grave to a small shrine and later, the first St. Peter's Basilica incorporated the original shrine into the floor of the altar.
However, twelve hundred years later, when the first basilica was replaced, the details of Peter's burial had been forgotten and though the Vatican had long held the traditional belief that Peter was buried under the basilica, even as late as the 1930s, they did not really have any clue about it.
The miracle happened in 1939, when the workers engaged to renovate the grottoes beneath St. Peter's Basilica, the traditional burial area of the popes, made a stunning discovery. Just below the floor level, they found an ancient Roman grave, an entire city of the dead. After months of uninterrupted digging, the excavators came near the area underneath the high altar, which contained the older graves. Finally, a large burial site was found just beneath the altar and in a niche connected to a wall painted red, they found the bones of a man.
On 26 June 1968, more than twenty years after the historic discovery, Pope Paul VI announced that the relics of Saint Peter had been discovered and on 24 November 2013, the relics were held by Pope Francis and displayed publicly for the first time after celebrating the closing of 'Year of Faith' Mass. The bones were placed in 19 transparent plexiglass containers, ten of which are in the niche in the wall.
However, there is no evidence Peter ever went to Rome. Regardless, when and where Peter died, he was unknown to anyone outside Jerusalem. Moreover, the traditional story about Peter’s death, reportedly crucified upside down in around 64 AD, did not start until long after his death. Actually, the Church spent centuries arguing over where to base its home. The Bishop of Rome was pushing for Rome and was helped when the said tomb of Peter was found in the city. It can also be argued that Peter’s skeleton was found in a space, which was previously known as a pagan graveyard. It may be argued that, Rome badly needed to find an important relic. Therefore, a body buried in a pagan cemetery was identified by them as the body of Peter and it was treated with respect and placed in a tomb. How they ascertained from a skeleton that the person was crucified, is also a question.
In fact, nobody knows for certain where the bodies of Saint Peter and Saint Paul lie, nor even if they are there at all.