Snow is on his first dive with a New York Police Scuba squad and is going into a waterway called the Cloaca Maxima. It's filled with sludge and debris with almost a zero visibility. He and the other divers are searching for a large brick of heroine that was part of a police shooting. While he doesn't locate the drugs, he finds two headless skeletal remains. The police officer in charge, Lieutenant Vincent D'Agosta, notes that the heroin has also been recovered but that it is now much less interesting. He tells the divers that they'll have to go back down to search for the heads.

The bodies are identified as Pamela Wisher, a young debutant, and Greg Kawakita, a young scientist. The body of Greg is badly deformed and both have what appears to be teeth marks, prompting an investigation. D'Agosta calls in scientists Dr. Frock and Margo Green. Green soon realizes that the teeth marks bear a resemblance to the murders of more than a year earlier, a monster that ate a specific plant. She soon figures out that the original scientist had ingested the plant which grossly deformed his body and created a need for a specific hormone which prompted him to kill in search of a supply of that hormone. Now Margo is faced with the challenge of finding out how the plant has survived and where it is growing. She, with the help of Agosta and FBI Special Agent Pendergast, soon learns that there is a population of people who have ingested a drug that's a byproduct of the Mbwun Plant and now live in the tunnels deep below New York City.

Prompted by a suggestion by Frock, it's decided that the tunnels will be flooded out. Then Margo discovers that the plant is actually being grown in the reservoir that will be used to flood the tunnel, meaning the population of creatures will have a ready supply of the plant. The use of grenades and other weapons are put into play and Margo uses vitamin D - deadly toxic to those who have ingested the plant - to kill many as the tunnels are flooded.

It's believed that the plan worked and that the creatures have been killed, but the bigger concern is that the plants would have leaked into the environment before a herbicide poured into the system could kill it. A year later, when there's no sign of an environmental catastrophe, Pendergast is finally able to smile.