An earthquake strikes the city of Los Angeles. Mike Roark (Tommy Lee Jones), the head of the city's Office of Emergency Management, insists on coming to work to help out with the crisis, even though he has taken a vacation with his daughter Kelly (Gaby Hoffmann). His associate Emmit Reese (Don Cheadle) notes the quake caused no major damage, but seven utility workers are later burned to death in a storm drain; one escapes and survives but is severely burned on one side of his face at MacArthur Park. As a precaution, Roark tries to halt the subway lines which run parallel to where the deaths took place, but Los Angeles MTA Chairman Stan Olber (John Carroll Lynch) declines, feeling there is no threat to the trains. Against regulations, Roark and a colleague Gator Harris (Michael Rispoli) venture down the storm sewer in the park to investigate. They are nearly burned to death when hot gases suddenly spew out of a crack in the concrete lining and flood the tunnel. Geologist Dr. Amy Barnes (Anne Heche) believes a volcano may be rapidly forming beneath the city with magma flowing underground (similar to the formation of the Mexican volcano Parícutin which emerged and grew tremendously in just one week) but cannot come up with enough evidence for Roark to take action.
Barnes and her assistant Rachel (Laurie Lathem) venture in the storm sewer to investigate the scene of the accident, where they discover a crack in the ground which released the gases earlier. While they are taking samples, a more powerful earthquake strikes and Rachel is killed when she falls into the crack. Near the La Brea Tar Pits, smoke rises out along with lava bombs. Steam explodes from the sewer system, while a subway train carrying passengers derails underground, trapping them inside and exposing them to severe heat and toxic gases, which cause them all to eventually pass out.
Minutes later, a newly formed volcano erupts from the tar pits and lava begins to flow freely down Wilshire Boulevard, incinerating and melting everything in its path, including Roark's truck and an LAFD fire truck, killing two firefighters trapped inside. Roark and his daughter become separated as she is injured when a nearby lava bomb burns her leg, and she is taken to Cedars-Sinai Medical Center by Dr. Jaye Calder (Jacqueline Kim). Meanwhile, Olber leads his team through the Red Line tunnel to the derailed train to look for survivors. They save everyone, but Olber notices that the train driver is still missing and goes back to find him. He finds the driver still alive but unconscious just as the lava reaches the train and begins melting it. Olber sacrifices his life to save the conductor by jumping into the lava flow, throwing the driver to safety as he is killed. Roark, Barnes, and police lieutenant Ed Fox (Keith David) devise a plan to stack concrete barriers at the intersection of Wilshire Boulevard and Fairfax Avenue, creating a cul-de-sac to pool the lava as helicopters dump water on it to form a crust. While the operation is successful, Barnes later theorizes that the magma is still flowing underground through the Red Line subway extension, and calculates that the main eruption will occur at the end of the line at the Beverly Center near Cedars-Sinai. To prove this, Dr. Barnes and Roark lower a video camera into the tunnel to watch it and then a fast-moving flow of lava incinerates the camera. They calculate the speed and is given 30 minutes until the lava hits the end of the red line.
Through Roark's direction, explosives are used to create channels in the street to divert the flow of lava into Ballona Creek, which will later flow into the Pacific Ocean, but Barnes realizes that the street is sloping in the opposite direction. Roark engineers another plan to demolish a 22-story condominium building (currently under construction by Jaye's husband) to block the lava's path from entering the city. When Gator refuses to abandon an LAPD SWAT cop who has gotten trapped under a core column while slotting explosive charges just as the lava reaches the dead end of the Subway tunnel extension and explodes out of the ground in a massive gyser, he sacrifices their lives to detonate the final explosive charge. Roark then spots Kelly nearby, trying to retrieve a small boy who wandered off, putting them in the path of the collapsing building. Roark barely manages to save both of them from being crushed as the building collapses. The plan is successful and the lava flows safely to the ocean.
The film's epilogue displays a graphic stating that the volcano, named "Mount Wilshire", is still in an active state.