Well, let us see! Holy Scripture does not deny that Peter was ever in Rome either, does it?
So nothing at all was gained by this charge, if you are a Sola Scriptura or Bible only believer.
Is Holy Scripture supposed to be "all encompassing", and the sole source for all historical facts?
Does it say that it is? Did you ever read John 21:25?
However, surprisingly, Holy Scripture does, in fact, say that Peter was in Rome...
"The Church which is at Babylon, chosen together with you, greets you, and so does my son Mark." 1Pet 5:13.
Where is this Babylon? By the time the New Testament was written, the city of Babylon, in what is now Iraq, was of almost no importance. Its days of glory were long past in the Old Testament.
Christians were under constant persecution by both the Jews and the Romans from the very beginning and had to practice the faith underground in the homes of believers, and in the catacombs of Rome. In order to recognize one another as fellow Christians, they used code words and symbols. The fish symbol (icthos) was used for recognition, and Babylon was the code word for Rome.
If Peter had said he was writing from Rome, then no doubt, the Romans would have begun an intensive search for him.
2. Holy Scripture tells us that the Roman Emperor Claudius (41-54) ordered all Jews to leave Rome (Acts 18:2). Peter was a Jew, but the Church was an underground Church in hiding at the time.
Well that charge to leave Rome, even implies that Peter could have been in Rome doesn't it?
Eusebius wrote in "The Chronicle" (Ad An Dom 42), that Peter, after establishing the Church in Antioch, went to Rome where he remained as Bishop of Rome for 25 years. We know from other early writings that Peter was crucified upside down in Rome in 67 A.D.. That date, minus 25 years would put him in Rome in the year 42, during the reign of Claudius. Again, this charge can be dismissed for the same reasons given already, that the Church was forced to practice the faith in an underground situation in order to avoid persecution. The Romans had a policy of hunting down and persecuting all of the Apostles.
Here are more genuine historical writings attesting to the fact that Peter was indeed in Rome, and that he died there...
St Irenaeus, "Against Heresies", 3,1,1, 180 A.D., J208
"...in their own dialect, while Peter and Paul were evangelizing at Rome, and laying the foundations of the Church."
St Irenaeus, "Against Heresies", chapter III,
"...the very ancient, and universally known Church founded and organized at Rome by the two most glorious apostles, Peter and Paul; as also [by pointing out] the faith preached to men, which comes down to our time by means of the successions of the bishops."
Eusebius, "History of the Church", 2,14,6, 300 A.D., J651dd
In the same reign of Claudius, the all-good and gracious providence which watches over all things guided Peter, the great and mighty one among the Apostles, who, because of his virtue, was the spokesman for all the others, to Rome."
Tertullian, "The demurrer against the heretics", chapter XXXII,1,
"...like the church of the Romans where Clement was ordained by Peter."
Who has the authority to ordain priests? Only Bishops do. Clement was ordained by the Bishop of Rome, Peter.
Saint Peter of Alexandria, "The Canonical Letter", canon 9, 306 A.D.
"Peter, the first chosen of the Apostles, having been apprehended often and thrown into prison and treated with ignominy, at last was crucified in Rome."
Eusebius, "The Chronicle" Ad An.Dom 68, J651cc
"Nero is the first, in addition to all his other crimes, to make a persecution against the Christians, in which Peter and Paul died gloriously in Rome."
Eusebius, "History of the Church", 3,2, 300 A.D., J652a
"After the martyrdom of Paul and Peter, Linus was the first appointed to the Episcopacy of the Church at Rome."