We read about Onesimus in Saint Paul's Epistle to Philemon, where we read that he had fled to Paul while he was in prison probably in Rome to escape punishment for a theft of which he was accused. After hearing the gospel from Paul, Onesimus converted to Christianity. Paul, having earlier converted Philemon to Christianity, sought to reconcile the two by writing the letter to Philemon. Some believe Onesimus was a servant of Philemon, and since Philemon was converted by Paul, Onesimus fled to Paul to mediate on his behalf.
We also come across the name Onesimus in Colossians 4, where we read that he accompanied Tychicus to Colossae. Whether or not these are one and the same person is unknown, but it is usually assumed they are.
According to the tradition of the Orthodox Church, the Apostle Onesimus is said to have died a martyr's death soon after the Apostle Paul was martyred, in the mid to late 60's A.D., in Potioli, Italy by having his legs beaten and crushed.
However, some believe he may also be the same Onesimus named by Ignatius of Antioch in his Epistle to the Ephesians as the Bishop of Ephesus, which would put Onesimus's death closer to 95 A.D. or even as late as 110.
Here we have the possibility of either one, two or three men named Onesimus. It is almost impossible to determine what is the truth, hence the mystery, but if we rely on tradition then it seems unlikely that the Onesimus mentioned by Paul is the same as the Onesimus mentioned by Ignatius. After all, it was a fairly common name at the time, and there is no reason to assume that everyone named Onesimus in the first century was the same person. But this is what New Testament scholar F.F. Bruce says:
“Why then should one connect the Onesimus who was the bishop of Ephesus about 110 with the Onesimus in the book of Philemon? Because Ignatius in his letter to the church at Ephesus shows himself familiar with the epistle to Philemon. It is one of the rare places in patristic literature where the language of our epistle is clearly echoed. Not only so, but the part of Ignatius’ letter to Ephesus where the language of Philemon is echoed is the part in which the bishop is mentioned in the first six chapters fourteen times.”
Going further than that, New Testament scholars like F. F. Bruce have suggested that it is Onesimus who was instrumental in collecting and preserving letters written by Paul, which were collected in the New Testament.
However, there are reasons to doubt the speculations of F.F. Bruce. First, tradition seems to contradict his claim. Second, Ignatius may have referred to the Epistle to Philemon in his letter only because the current Bishop of Ephesus Onesimus reminded him of the Onesimus mentioned by Paul, and therefore it was done as a rhetorical device. Third, Ignatius never associated or connected Onesimus of Ephesus with the Onesimus that was a disciple of Paul. Fourth, there is no tradition linking Onesimus with being a Bishop of Ephesus.
The mystery remains a mystery and one could only speculate what the truth is.