When Nier and Grimoire Weiss first come to the Junk Heap, they encounter the two brothers, Jakob and Gideon, who live in a shack right outside. Nier talks to them about strengthening his weapon, and is asked to retrieve three Titanium Alloys from inside for Jakob to work with. Nier complies and goes inside the Junk Heap, fighting many guard robots that attack the party. After collecting three of them, Nier returns to the brothers' shop. After Gideon cries about his missing mother, Jakob reluctantly asks Nier to help them find her. He goes deep within the Junk Heap to search for the missing mother. After going to the bottom and defeating Defense System Geppetto, they find the missing mother's body, along with that of her lover.
In the second part of the game, a flashback is shown of Gideon and Jakob going into the Junk Heap. Gideon accidentally causes his brother's death, but blames it on the shade and robot nearby. When Nier goes back to the area, he is asked to destroy the robot and shade that Gideon believes killed his brother. The shade and the robot are found at the bottom of the Junk Heap and destroyed.
- All characters found in the Junk Heap are named after characters from The Adventures of Pinocchio.