As the employees of Global Dynamics complete Dr. Anne Young's seminar on sexual harassment, Allison asks Jack to locate biological systems engineer Dr. Stone, who hasn't come in to work. The eccentric scientist lovingly maintains a network of Eureka's utilities, including air conditioning and waste processing, that is inspired by the human digestive system. Without Stone constantly fine-tuning the system in the tunnels below town, things will go haywire. Methane buildups, for example, might cause toilets to explode … which is exactly what happens, moments later, at the Sheriff's Office.
After interviewing Stone's wife and visiting the tunnels, Jack stops in at Café Diem. There, bizarrely, Jo Lupo flirts with him. Even when another overload in the system causes a messy explosion in the restaurant, Lupo is undeterred: she grabs Jack and kisses him.
As Jack flees to Global Dynamics and Lupo wonders what on earth came over her, a geyser of water erupts downtown. Time is running out for Eureka's bowels, so Jack intensifies his search for Stone. Deep within the tunnels, he discovers a pile of bones dusted with mysterious powder. He brings them to Jim Taggart for analysis, then reports to Allison. Allison, however, can't concentrate: she's overwhelmed by attraction for Jack. So is Dr. Young. The next thing Jack knows, the two women are fighting a pitched battle over him.
Jack escapes to Taggart's lab, where Taggart announces that the bones belonged to ancient humans who apparently tore each other apart. Allison and Young, meanwhile, recover their sanity as soon as Jack's gone. They analyze a sample of his blood and discover that his body is overproducing a hormone that stimulates sexual attraction.
Although the notion that he's irresistible to women freaks him out - sort of - Jack doesn't let it stop him. He investigates the Stones' house and finally finds the missing scientist locked in the bedroom. Mrs. Stone had imprisoned her husband because she was overcome with desire for him. Fresh from this pleasant captivity, Stone is dismayed to learn that he only got lucky because he's suffering from the same hormone imbalance as Jack.
While Stone struggles to repair the town's ailing systems, Taggart discovers that the mysterious powder consists of ancient spores. Jack and Stone inhaled it in the tunnels, activating the spores, which in turn caused the hormone imbalance. Worse, the women affected are inexplicably beginning to turn violent. If the spores can't be neutralized, Jack and Stone will be ripped to shreds just like their pre-historic counterparts.