The first mention of Jesus is in book 18 of Jewish Antiquities. Historians are largely agreed that the passage in question has been tampered with by a later Christian scribe. However, at least part of the passage is widely believed to be authentic. The words in bold below are thought to be the additions of a Christian scribe trying to make Jesus appear in a better light than Josephus would have wished.
Now there was about this time Jesus, a wise man, if it be lawful to call him a man; for he was a doer of wonderful works, a teacher of such men as receive the truth with pleasure. He drew over to him both many of the Jews and many of the Gentiles. He was the Christ. And when Pilate, at the suggestion of the principal men amongst us, had condemned him to the cross, those that loved him at the first did not forsake him; for he appeared to them alive again the third day; as the divine prophets had foretold these and ten thousand other wonderful things concerning him. And the tribe of Christians, so named from him, are not extinct at this day. (Josephus, Jewish Antiquities, 18, 3, 3)
To support the idea that the passage is partly authentic and partly interpolated, we can look at the works of a 3rd-century Christian father called Origen. He lived while Christianity was still a minor cult with no power or influence. Its adherents were generally ignored by the authorities as long as they kept their heads down. Therefore, there is no way that Christians this early could have secured every copy of Josephus so that no undoctored copies remained, or could have gotten away with quoting something from Josephus that was not there. So we can be sure that the copy of Josephus that Origen read and quoted from had not been amended by earlier Christians. We can be doubly sure of this because Origen flatly contradicts the modern version of Josephus where the Jewish historian is made to say Jesus was the Messiah. Origen makes clear he said no such thing.
What use would the early fathers have had for a passage in Josephus saying Jesus was not the Messiah? An educated Jew stating this would not be helpful, as it would demonstrate that the prophecies in the Old Testament were not nearly as clear-cut as early Christians would have liked to believe. And because no early skeptics or opponents of Christianity ever challenged Jesus' existence, early Christians never had any reason to point to a critical Jewish source to prove that he was real. Hence Josephus was not quoted by earlier Christian writers.
So what exactly did Origen write? Here are two passages from his works. Both of them basically say the same thing and reinforce each other:
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 such 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, although 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 X, XVII)
For in the 18th book of his Antiquities of the Jews, Josephus bears witness to John as having been a Baptist, and as promising purification to those who underwent the rite. Now this writer, although 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)—the Jews having put him to death, although he was a man most distinguished for his justice. (Origen, Against Celsus I, XLVII)
The second mention of Jesus by Josephus is a much briefer reference to "James, brother of Jesus called Christ." We also know about James from the Acts of the Apostles and the letters of Paul. He was indeed Jesus' brother and one of the early leaders of the Church. This second mention of Jesus certainly existed in Origen's copy of Josephus because Origen uses the phrase "called Christ" twice. It cannot be a Christian interpolation into Josephus because Christian texts called James either "James the Just" or "James the Brother of the Lord."
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