As revealed in Grimoire Nier, the Hamelin Organization was an international organization formed in December of 2016, after it was discovered that the anti-WCS drug "Luciferase" was more effective with younger patients. Their goal was to find children with high physical ability and receptiveness to Luciferase, to use as soldiers to combat the Legion threat. Their methods were sometimes immoral; it is implied they abducted orphaned children and coerced them into service as soldiers, lied to the children about the effectiveness of Luciferase, and even pitted them against one another in secret experiments involving magic. They later expanded to include Project Gestalt and the World Purification Organization.
The Hamelin Organizations soldiers were organized into units known as "Crusades". Their first unit was the 5th Crusade; four previous units had fought and died against the Legions before the organization was formed. The 13th Crusade, likely the final of such units, was finally able to destroy the leader of the Legions and thus greatly reduce their threat to humanity. It is noted that the leader of the 13th Crusade died from injuries sustained in the final battle.
- The name of the Hamelin Organization is a reference to a folk tale, the Pied Piper of Hamelin, in which a man who was hired to charm the rats out of the town of Hamelin later charmed their children away in response to their refusal to pay him for his work.