In the Sparrow, Emilio returns to earth a broken and shattered man. In the Children of God, Emilio is helped by his Jesuit peers, but healing truly begins when he leaves the priesthood and falls in love with Gina. But, unfortunately, Emilio will not be left alone. He is kidnapped and put back on a ship to return to Rakhat.
In his absence, revolution has come to Rakhat through the presence and work of Sofie Mendes Quinn who was marooned on Rakhat. The Runa now rule most of the planet. Emilio arrives in time to convince Sofie and others to let the remaining Jana'ata live.
Living amongst the Jana'ata is Isaac, Sofie's son. He is autistic and is drawn to the chant music of the Jana'ata.
Emilio returns to earth. Gina has died. But, he meets his adult daughter and grandson.
A couple of themes that began in The Sparrow continue through the Children of God. The first is that there are always unintended consequences when one culture intermingles with another. Cultures have different assumptions about nearly everything. In a sense, both books are a meditation on what can go wrong when one culture invades another. The second is forgiveness. Emilio learns to forgive his family of origin, then his captors and rapists on Rakhat, then those who kidnapped him for the second trip to Rakhat. The man who meets his daughter in the final pages of the book is a man who embodies God's grace and peace.