The story picks up where the epilogue of Relic left off. Two headless skeletons are found in the Humboldt Kill. When further decapitated bodies follow, there is suspicion of a second Mbwun monster. Major characters from the original book team up with new ones to solve the puzzle. The mystery soon leads underground to the Mole people, and even deeper towards enigmatic beings called the Wrinklers.
In the end, it is revealed that the Wrinklers are led by Frock, who has refined a modified version of the Mbwun plant, created by Kawakita to regain the use of his legs. Kawakita also gave the drug to the people who were to become the Wrinklers, later made into his tribe by Frock. After going underground, the group kills them with an explosion, vitamin D infused water and a flood.