In Book 20 of Josephus' Antiquities there is what could be called a passing reference to Jesus in a paragraph describing the murder of Jesus' brother, James, at the hands of Ananus, the High Priest.
But the younger Ananus who, as we said, received the high priesthood, was of a bold disposition and exceptionally daring; he followed the party of the Sadducees, who are severe in judgment above all the Jews, as we have already shown. As therefore Ananus was of such a disposition, he thought he had now a good opportunity, as Festus was now dead, and Albinus was still on the road; so he assembled a council of judges, and brought before it the brother of Jesus the so-called Christ, whose name was James, together with some others, and having accused them as lawbreakers, he delivered them over to be stoned.
Jewish Antiquities 20.9.1 (emphasis added).
According to the leading Josephus scholar Louis H. Feldman, the authenticity of the reference to Jesus and James "has been almost universally acknowledged" by scholars. Feldman, "Josephus," Anchor Bible Dictionary, Vol. 3, pages 990-91. Indeed, of the few commentators who challenge the authenticity of this reference to Jesus, most are proponents of the Jesus Myth. Obviously, it will not due to let this one reference in Josephus sink their entire theory (and in some cases, apparent mission in life). I will not here recount all of the arguments concerning authenticity, but want to address the issue of Origen's knowledge of the passage.
Origen, a Christian writer of the early third century, refers to the martyrdom of James in Josephus' Antiquities:
And to so great a reputation among the people for righteousness did this James rise, that Flavius Josephus, who wrote the 'Antiquities of the Jews' in twenty books, when wishing to exhibit the cause why the people suffered so great misfortunes that even the temple was razed to the ground, said, that these things happened to them in accordance with the wrath of God in consequence of the things which they had dared to do against James the brother of Jesus who is called Christ. And the wonderful thing is, that, though he did not accept Jesus as Christ, he yet gave testimony that the righteousness of James was so great; and he says that the people thought that they had suffered these things because of James.
Origen, Commentary on Matthew 10.17 (emphasis added).
In Against Celsus 1.47, Origen wrote:
[A]lthough not believing in Jesus as the Christ, in seeking after the cause of the fall of Jerusalem and the destruction of the temple, whereas he ought to have said that the conspiracy against Jesus was the cause of these calamities befalling the people, since they put to death Christ, who was a prophet, says nevertheless-being, although against his will, not far from the truth-that these disasters happened to the Jews as a punishment for the death of James the Just, who was a brother of Jesus called Christ.
These passages reveal obvious familiarity with the Josephan reference to James. But what of his reference to the wrath of God falling on the Jewish people because of the treatment of James the brother of Jesus? No such explicit statement is found in Josephus' reference to James or Jesus. Other Christian writers, most notably Eusebius, repeat it without giving any specific indication of where in Josephus it was written (most likely under Origen's direct or indirect influence).
G.A. Wells has suggested that this is evidence of tampering—that Origen knew of a version of Josephus' writings that had already been corrupted with an interpolation by Christian scribes. Wells, The Legend Legend, at 54. His intent is to cast doubt on the passage by conjuring up supposed evidence of further tampering by eager Christian scribes desperate to rewrite Josephus. Earl Doherty too argues, for his own reasons, that there was a Christian interpolation claiming the murder of James was the cause of the destruction of the Temple that disappeared from the manuscript traditions. Doherty, The Jesus Puzzle, at 219.
A more likely explanation is that Origen simply read into Josephus’ statements about James an earlier, independent Christian tradition--as attested by Hegesippus and Clement of Alexandra--linking James’ death with the destruction of Jerusalem and the Temple. After all, writing to explain the war was one of Josephus' purposes. And such an approach to Josephus would be consistent with Origen’s exegetical and writing styles. He is notorious as an imaginative reader of texts. Josephus’ writings were not an exception as Origen tended to read Christian traditions into Josephus’ writings. Alice Whealey, Josephus on Jesus, at 17-18.
Furthermore, the placement of the martyrdom of James in Antiquities would have given Origen all the reason he needed to read the account of James' martyrdom in light of the destruction of Jerusalem. The martyrdom is described just before Josephus begins to discuss the problems that lead to the war with Rome, whose legions destroyed Jerusalem and the Temple. Just a few lines after describing James' death, Josephus writes, "this was the beginning of greater calamities...." Ant. 20.3. A few lines after that, Josephus writes, "And from that time it principally came to pass that our city was greatly disordered, and that all things grew worse and worse among us." Ant. 20.4. While Josephus was referring to other events, the proximity to the killing of James must have proved irresistible to Origen. It is also possible that Origen conveniently confused Josephus' explicit statement that Herod's execution of John the Baptist lead to God's judgment with the High Priest' execution of James leading to God's judgment.
Origen elsewhere shows that he is willing to read Josephus loosely but recount it as something stated by Josephus. In Fragment 115 of Origen’s Commentary on Lamentations, Origen comments on verse 4:19 (“Our pursuers were swifter than the eagles of the sky; they chased us on the mountains, they waited in ambush for us in the wilderness."), stating that “Josephus reports that even the mountains did not save those who were trying to escape.” There is no such explicit statement in Josephus’ writings, though it may be an inference from both of Josephus’ descriptions of the fall of Jerusalem. As Wataru Mizugaki notes, “by citing and using Josephus to his own purposes, Origen interprets [Josephus’] historical account from his theological viewpoint and adapts it to his interpretation of the Bible.” Mizugaki, “Origen and Josephus,” in Josephus, Judaism, and Christianity, at 333.
That Origen took Josephus' broader purpose of explaining the causes of the Jewish War, read nearby statements about the beginning of troubles and calamities a little loosely, and read into the account of James' martyrdom the existing Christian tradition about James' death being a cause of God's judgment, is the most likely explanation as to the origins of Origen's comments about James and judgment in his Commentary on Matthew and Against Celsus.