It is true that some legendary traditions exist referring to the deaths of the disciples, but not for all of them and their associates. We have some evidence for other early Christians who never recanted their faith in Jesus even in the face of death. We will briefly acknowledge the evidence we have for this claim.
In chapter 5 of a Letter to the Corinthians composed by the early church father Clement of Rome (35-99 CE), writing around 95-97 CE, he speaks of the Apostle Paul’s martyrdom. According to Clement, Paul “suffered martyrdom under the prefects.” Such a detail is not inconsistent with what we find in Paul’s own letters in which he refers to himself suffering willingly for Jesus. Paul faced death several times in his journeys (2 Cor. 6:5). Clement is knowledgeable of the events of the early Church and there is little reason to distrust his testimony. He was also an associate of Peter and Paul met both Peter and James, which suggests a good possibility of early, insider information. Clement’s letter referring to Paul’s martyrdom was written early and probably at the same time of the book of Revelation (around 95 CE) in the first century.
An additional piece of evidence perhaps pointing to Paul’s death as a martyr is found in 2 Timothy which dates to 90 CE or after and is found in the New Testament; the text reads: “For I am already being poured out as a drink offering, and the time of my departure has come. I have fought the good fight, I have finished the course, I have kept the faith” (4:6-80). Importantly, 2 Timothy is not held by scholars to be a genuine Pauline epistle, but rather a letter written by someone else, perhaps a disciple of Paul’s. Whoever wrote this relevant text does, however, show knowledge of Paul’s death. It reads as if Paul had come to the end of his life and that he is reflecting on his past deeds. He believes his life had been a living sacrifice presented to God.
We are on reasonably good grounds historically to affirm Paul’s martyrdom as a fact of history. There is first-century testimony by Clement and Second Timothy, and a death seems consistent with what we know about Paul’s wider missionary activities which included his imprisonment, flogging, abuse, and more. In light of this, Paul’s martyrdom was always a likely possibility.
Moving on, we are told of the martyrdom of Stephen in the New Testament book of Acts:
“[They] dragged him out of the city and began to stone him. Meanwhile, the witnesses laid their coats at the feet of a young man named Saul. While they were stoning him, Stephen prayed, “Lord Jesus, receive my spirit.” Then he fell on his knees and cried out, “Lord, do not hold this sin against them.” When he had said this, he fell asleep” (7:58-60).
Stephen is thought to have died around 34 CE which is just a few years after Jesus’ death. Acts was written around the 70s to 80s CE, so is around half a century after the fact, which we can consider early when it comes to ancient history.
We are also told that James, the brother of John, was put to death by Herod in Acts: “It was about this time that King Herod arrested some who belonged to the church, intending to persecute them. He had James, the brother of John, put to death with the sword” (12:1-2).
Thirdly, we have an account of Jesus’ brother (Mark 6:3; Matthew 13:55), James, being martyred in the work of Josephus Flavius, a first-century Jewish historian who is our primary source for first-century Jewish history and religious figures. According to Josephus,
“[They] brought before them the brother of Jesus, who was called Christ, whose name was James, and some others; and when he had formed an accusation against them as breakers of the law, he delivered them to be stoned” (Antiquities 20 v.9).
Josephus provides an independent reference to Jesus and the death of James. Josephus obtained his information from a source outside that of the New Testament, as suggested by the fact that the New Testament itself does not refer to James’ death.
It is important to consider James, the brother of Jesus, in light of Jesus’ family believing him to have lost his mind. In Mark 3:21 we read that: “When his family heard about this, they went to take charge of him, for they said, “He is out of his mind.” In John’s gospel, we read that “not even his brothers believed in him” (7:5) and Jesus was also rejected by his hometown Nazareth (Luke 4:14-30). The response of Jesus’ family, who thought him mad for thinking himself to be the Messiah, becomes very interesting when we later consider that his skeptical brother James became a pillar and major leader in the early Church (Acts 15). His mind seems to have changed after the risen Jesus is said to have appeared to him (1 Cor. 15:7). It is this belief that, as we learn from Josephus, had Jame martyred.
The apostle Peter’s death was seemingly foretold by Jesus in the Gospel of John:
“Very truly I tell you, when you were younger you dressed yourself and went where you wanted; but when you are old you will stretch out your hands, and someone else will dress you and lead you where you do not want to go.” Jesus said this to indicate the kind of death by which Peter would glorify God. Then he said to him, “Follow me!” (21:18-19).
John’s gospel was written around 90 CE, which will have many scholars, who reject that Jesus could predict the future accurately (whether by supernatural means or a guess), seeing this as John reflecting knowledge of Peter’s death and putting these words on the lips of Jesus. Clement of Rome also mentions Peter’s death in his Letter to the Corinthians: “There was Peter who by reason of unrighteous jealousy endured not one but many labors, and thus having borne his testimony went to his appointed place of glory” (chapter 5). Peter’s death is also attested to by Tertullian (lived 155-240 CE) at the end of the second century, and by Origen in Eusebius of the fourth century.
To summarize: Historically, it is reasonable to accept the martyrdom of Paul, Stephen, Peter, James (brother of John), and James (brother of Jesus): Paul’s death is affirmed by the testimony of Clement and Second Timothy; Stephen by Acts; Peter by the Gospel of John and Clement; James, the brother of John, by Acts; and James, the brother of Jesus, by Josephus Flavius.
Foakes Jackson, F. J. 1927. “Evidence for the Martyrdom of Peter and Paul in Rome.” Journal of Biblical Literature 46(1/2):74-78.