Father Emilio Sandoz is a Jesuit priest who has returned to Earth and is recovering from his experiences on the planet Rakhat (detailed in The Sparrow).

This news caused a rift between the Society of Jesus and the rest of the Catholic Church, and the Jesuits are determined to return to Rakhat and help the Runa.

When Emilio Sandoz and the Jesuit mission finally arrive on Rakhat, they find that the Runa revolution has succeeded and most of the Jana'ata have been wiped out.

The Jesuit Danny Iron Horse, a Lakota, suggests arranging an Indian reservation-like setup for the remaining Jana'ata on Rakhat.

Isaac stays in the valley with Ha'anala's children and continues his mysterious project, creating music by overlapping the genomes of all three sentient species, and finds patterns that he believes are evidence of the existence of God.

[1] A Publishers Weekly review determined Russell "uses the entertaining plot to explore sociological, spiritual, and scientific questions.

[2] Reviewing the novel in National Catholic Reporter, novelist Valerie Sayers felt that Children of God focuses on the problem of evil.