Adam Pierce, a technician at the California Institute of Technology's Volcano Observatory, approaches Mulder and Scully with a mystery. A team of scientists working at Mount Avalon issued a distress signal requesting an immediate airlift. When contact with the team was lost, Pierce and his fellow scientists at Cal Tech activated a robotic camera, nicknamed Firewalker, which relayed pictures from inside an active volcano. The pictures--which are reviewed by Mulder and Scully --show Chief Seismologist Phil Erikson's heat-seared corpse lying at the volcano's caldera, where temperatures reach over 400 degrees Celsius. The videotape also captured a hulking figure near the body. Pierce suspects that his brilliant colleague, Daniel Trepkos, may somehow be responsible for the death.

Mulder, Scully and Pierce fly by helicopter to Mount Avalon. They find scientists Jason Ludwig, Jesse O'Neil and Peter Tanaka hiding inside the field base. Ludwig describes how Trepkos went berserk and destroyed the facilities. Shortly thereafter, Trepkos finds Pierce and strangles him. Mulder uncovers Trepkos' notes, which describe an unknown life form living inside the volcano. The notes suggest Trepkos possesses physical evidence that proves the existence of silicon-based life. Scully interviews Jesse O'Neil, who had been romantically linked to Trepkos.

Tanaka begins having coughing fits. Scully insists he be airlifted off the base and taken to a hospital. However, the scientist runs off into the forest. Mulder and Ludwig give chase. Tanaka loses his balance and trips, falling down an embankment. Suddenly, his throat swells enormously and a spike-shaped protrusion pierces his skin, killing him instantly. Scully's examination of the body supports Mulder's theory that a silicon-based life form, possibly a fungus, grew inside Tanaka's body. Believing the fungus to be communicable and airborne, the group is quarantined.

Ludwig volunteers to guide Mulder to the underground steam caves where Trepkos is believed to be hiding. Trepkos surprises them and shoots Ludwig with a flare gun. He proceeds to burn the body so that the parasitic spore living inside will die. Trepkos explains the Erikson inadvertently released the spore after Firewalker pulled a sample out of the volcano. Everyone at the base -- except himself -- was infected by the parasite. He crippled the transmitter equipment, and killed Pierce in an effort to keep the spore from spreading. Mulder, sensing Scully is in jeopardy, races back to the base.

O'Neil handcuffs herself to Scully and loses consciousness. Realizing what is about to occur, Scully carries her body to the rubber-sealed Plexiglass door and places her on the other side to separate them. O'Neil's throat expands to grotesque proportions. Suddenly, O'Neil's throat explodes, the organic matter spattering against the Plexiglass. Mulder finds Scully safe and unharmed.

Trepkos returns to the base, where he discovers Jesse's corpse. Mulder allows him to remove the body and leave the area. Meanwhile, he and Scully are quarantined for a month to ensure neither has been infected.