The Church Letter is the letter that is found by the fathers of the Origami Killer's victims before they are kidnapped. It's in an addressed envelope written by a Royal 5 typewriter. Ethan Mars receives the letter in the third chapter.
The text of this letter is likely a reference to the Pied Piper of Hamelin, in which a man first leads a lot of rats to their death by attracting them to the music of his pipe and driving them into a river and then lures all the children of the town into a cave.
When the parents came home from Church
All their children were gone.
They searched and called for them,
They cried and begged,
But it was all to no avail.
The children have never been seen again.