The Alleluia Files is the third book in the Samaria Trilogy, set over a hundred years after the events of that novel.

The Archangel Bael is hunting down Jacobites and performing tortures and executions on them to try and destroy the movement. They believe that Jovah is really a space ship called Jehovah, and that the Oracle Alleluia left files proving it.

Lucinda is an angel, and Tamar is a Jacobite, but despite this there is an old tie there that neither know about. Bael knows, and he will do anything to destroy Tamar and bring Lucinda to heel before things get out of hand. His tenure as Archangel is coming to an end and he is reluctant to part with it, hoping to install his human son as the consort of the next Archangel.

When the angel Jared hears of what is happening to the Jacobites, he is horrified that Bael would actually kill people. He sets himself to learn the truth about what is happening, and about the Jacobites, and soon meets Tamar. Despite his best efforts, she does not trust him, and fears for the safety of her friends.

Only when Lucinda and Tamar meet do they come to understand the truth about Bael and his obsession with the Jacobites.