The three passages appear in separate sections of the Antiquities. The short Jesus notice comes first, followed by the longer accounts of John and the execution of James. Leaving the controversial Testimonium to last, let us first examine John and James, both in their Josephan context and in comparison with the corresponding Christian sources.

John the Baptist

In the Gospels, John, an eremitic prophet, preached repentance and baptism in the wilderness of the Jordan. He was the forerunner of Jesus, his follower and successor in Galilee. John was imprisoned and beheaded on the occasion of the birthday feast of the ruler of Galilee, Herod Antipas, for disapproving of his marriage to Herodias, his sister-in-law.  Josephus mentions no link between John and Jesus, places the venue of John's execution not in Galilee, but in Machaerus (Mukawir), a fortress in contemporary Jordan, and does not connect the downfall of the Baptist with his disapproval of the union between Antipas and Herodias. For Josephus, John was an exemplary character, a "good man", who "had exhorted the Jews...to practise justice towards their fellows and piety towards God, and so doing to join in baptism". He noted, however, that John "aroused" his followers to the highest degree by his sermons. The word "aroused" implies that he was a powerful and fiery preacher, and as such capable of igniting a revolt. 

So, Josephus continued, Antipas decided to "strike first and be rid of him before his work led to an uprising". The eloquent John was seen by Antipas — like Jesus, one may add, by the high priests after he had caused mayhem in the merchants' quarter in the Temple — as a potential threat to civic order. In consequence, both were eliminated. 

Josephus included John's story in his narrative because the annihilation of Antipas's army by Aretas, the Nabatean king and the enraged father of the wife abandoned by Antipas for Herodias, was interpreted by the Jews as a divine vindication that fairly closely followed John's murder. There is no reason to suspect here a Christian hand. The account fits Josephus's narrative style and explains the tragedy just as well as the anecdote of Herodias's dancing daughter, Salome, demanding the head of the Baptist on a platter. Against the Gospel version note that Machaerus on the distant Nabatean border would be a rather unsuitable location for a royal birthday party intended for the Galilean nobility (Mk 6:21).

James, the brother of Jesus

The authenticity of the mention of James is the least questionable of the three anecdotes. Josephus identifies James not as the son of "X", but as "the brother of Jesus who was called the Christ". Paul also refers to him as "James the brother of the Lord". The atmosphere of the story reflects the political situation in Jerusalem in the first century CE, with Roman governors and Jewish high priests constantly vying with one another for power.