It may simply be omission that Yom Kippur is not mentioned in the rest of the Bible. But in the passages dealing with events observed during the month of Tishri, the silence on the Day of Atonement is glaring.The evidence he collects is compelling and it is clear that the Day of Atonement was not celebrated in the pre-Exilic Temple cult or even during the Exile and into the early Restoration period. His guess that it was established around 400 BCE is plausible. Mr. Gilad then suggests the following:
The Roman-Jewish historian Josephus Flavius recounts a story pertaining to these individuals, which may hold the key to the origins of Yom Kippur.Maybe. But we should be cautious. Josephus was writing centuries after the events he described and we don't what his source was or if it is reliable. He includes quite a few stories in the Antiquities which are obviously legends and this may be one too. Moreover, even if the story is true, it is speculative, if not implausible, to connect it to the founding of the Day of Atonement. It really only pushes much of the problem back a step, leaving us to ask how the priests thought they could introduce a new festival into the calendar as though it were an old one, and where the ritual in Leviticus 16 came from in the first place.
When Nehemiah arrived in Jerusalem in 444 B.C.E., he found that the Jews in the city were mixing with the local population. Even worse, Jeshua, son of Joiada the high priest and heir to the priesthood, married the daughter of his enemy Sanballat the Horonite, governor of Samaria: “And one of the sons of Joiada, the son of Eliashib the high priest, was son in law to Sanballat the Horonite: therefore I chased him from me,” he writes (Nehemiah 13:28). When Joiada died, Nehemiah replaced him with Jeshua’s younger brother, Johanan. But then, in 413 B.C.E., Nehemiah himself died.
According to Josephus, in his book “The Antiquities of the Jews,” Bagoas conspired with Jeshua to have him replace his younger brother as high priest. When Johanan learned of this, he confronted his brother in the Temple and killed him. When Bagoas subsequently heard what had happened, he rushed to the Temple. “Have you had the impudence to perpetrate a murder in your temple!” Bagoas shouted as he made his way into the holy sanctuary. Those in attendance pleaded with him not to enter as his presence would defile the Temple. He ignored their cries, declaring, “Am not I purer than he that was slain in the temple?”
Josephus doesn’t say what happened after this shocking event took place. But clearly, this was a huge crisis. The Temple had to be cleansed, but how?
After looking through the Bible and not finding reference to a ceremony that could make amends for what had happened, Johanan and his fellow priests must have looked elsewhere, until they found the text that constitutes what is now the bulk of Leviticus 16, describing the ritual carried out by Aaron.
Again, it's an interesting idea and I can't prove it's wrong, but I think it is historically more plausible to look for the origins of new festivals in new social trends than in a specific event.
Mr. Gilad published an article last year exploring the possible connection of the Day of Atonement to the Mespotamian spring New Year festival, the Akitu. This is possible as well. I give my own very tentative view of the origins of Rosh HaShanah and Yom Kippur in this post. This is not so much a theory as a notion, but it still makes sense to me.