Two early Church authorities, Origen and Eusebius, report that Josephus believed that the calamity of the Jewish uprising was visited on the Jews by God because they had murdered James the Just. But this passage is no longer extant in any manuscripts of Josephus’ works.
It is not a variant or mistaken quote of the passage in which Ananus is blamed for having James (whether or not the same James) stoned to death. This is because Eusebius quotes both this passage (as it now appears in Antiquities) and a second presumed lost passage as follows:
These things happened to the Jews to avenge James the Just, who was a brother of Jesus who is called Christ, for the Jews slew him, although he was a most just man.
Many have argued that this must have been an interpolation (then removed at some later point), with one or the other passage originally being the source for the other. It is clear that ‘who was a brother of Jesus who is called Christ’, present in both passages, (see The wrong stoning) would have been a Christian interpolation. The same goes for the phrase ‘the Jews’, more akin to the style of the Gospel of Peter than that of Josephus who was a Jew.
We are really asking the wrong questions.
So, here are a few. James is a towering figure, from the description in Acts, the writings of early Church (patristic) authorities, Ebionite sources and possibly the commentaries on Habakkuk and psalm 37 in the Dead Sea scrolls. So why does Josephus fail to give him no more than a passing mention? Or, quite likely, if the passage that is in Antiquities refers to another James, no mention at all?
Jesus likewise gets no reliable (non interpolated) mention. He would not have been a very successful rebel in Josephus’ eyes. That is, assuming that Jesus/Yeshua is an historical figure. Which I judge on the evidence to be the case.
But why no mention of Jesus at all?
At precisely the point in Antiquities where there should have been a description of the Jesus story, Josephus has two mocking tales, one an apparent satirical attack on Saul/Paul and one a parody of the Christian gospel myths (see chapter 9 of Jesus the terrorist). The precise placing is, I suggest, an acknowledgement that something involving a character called Jesus happened at that time.
These and other omissions and the mixing up of information on messianic contenders is an indication that Josephus saw his role as limited (as stated in his Jewish War) to providing a warning against rebellion to subject peoples. He saw no need to deliver up to Rome others in what I have described as a submerged messianic line.
But, if not from Josephus, where did the idea originate – that the death of James might have been closely involved with the calamity of the Jewish uprising? It could have been an inherited, common presumption. Not a likely one, if James died in CE 62, four years before the war. More likely, if his death had happened nearer to the outbreak of hostilities, with James and his role and his demise among a number of factors.that Josephus carefully avoids mentioning.
But he does record that Ananias was fairly swiftly caught and killed by the insurgents, perhaps ‘to avenge James’.