Geophysicist Dr. Josh Keyes (Aaron Eckhart) and scientists Dr. Serge Leveque (Tchéky Karyo) and Dr. Conrad Zimsky (Stanley Tucci) become aware of an instability of Earth's magnetic field after a series of bizarre incidents across the globe. They determine that the Earth's molten core, which generates this field, has stopped rotating and that, within a year, the field will collapse, exposing the planet's surface directly to devastating solar radiation. Backed by the U.S. Government, Keyes, Leveque, and Zimsky create a plan to bore down to the core and set off several nuclear explosions to restart the rotation. They gain the help of rogue scientist Dr. Ed "Braz" Brazzelton (Delroy Lindo), who has devised a vessel made of "Unobtainium" that can withstand the heat and pressure within the Earth's crust and convert it to energy, as well as a laser-driven boring system that will allow them to quickly pass through the crust.
Construction starts immediately on the Virgil, a multi-compartment vessel to be helmed by Space Shuttle Endeavour pilots Commander Robert Iverson (Bruce Greenwood) and Major Rebecca "Beck" Childs (Hilary Swank), who will join Keyes and the others. To prevent a worldwide panic, Keyes enlists computer hacker Theodore Donald "Rat" Finch (DJ Qualls) to scour the Internet and eliminate all traces of the pending disaster or their plan.
Virgil is launched through the Marianas Trench from an offshore platform. The team accidentally drills through a gigantic empty geode structure 700 miles below the surface, damaging the lasers when it lands at its base and cracking the geode's structure and causing magma to flow in from above. The crew repair and restart the laser array in time, but Iverson is killed by a falling crystal shard that hits him in the helmet and subsequently fell into magma, while returning to the ship. As Virgil continues, it clips a huge diamond that breaches the hull of the last compartment. Leveque sacrifices himself to save the nuclear launch codes before the compartment is crushed by extreme pressure.
Meanwhile, on the surface, the public becomes aware of problems after a lightning superstorm and an unfiltered patch of ultra-violet radiation from the sun destroy Rome and San Francisco, respectively. Finch is unable to stop worldwide panic but instead learns of the top-secret project "DESTINI" (Deep Earth Seismic Trigger INItiative), which is the government's 'secondary protocol' and will be deployed should the Virgil mission fail. Finch relays his information to Keyes, who discovers that Zimsky was one of DESTINI's lead scientists. DESTINI, according to Zimsky, was designed as a weapon to propagate earthquakes through the Earth's core, but its first activation unintentionally stopped its rotation instead. Zimsky reveals the government will use it again to attempt a restart of the core. Keyes is convinced it will have disastrous results and has Finch hack into DESTINI's system and cut its power supply to buy the Virgil more time.
Virgil eventually reaches the molten core, and, as they take readings, they discover that the density of the core is far different from what they expected, which will not allow their plan to work. They calculate that by splitting their nuclear weapons into the remaining compartments and jettisoning each at specific distances, they can create a "ripple effect", where the power of each bomb will push against the blast of the next, generating the energy required to restart the core. However, because Virgil was not designed to jettison undamaged compartments, the plan requires someone to deactivate a safety switch that is in an area exposed to the extreme temperatures. Brazzelton volunteers and deactivates the switch, dying shortly afterwards.
Keyes and Zimsky race to reset the nuclear charges, and Zimsky gets trapped in one of the detaching compartments. Keyes believes they still may have too little yield, but Zimsky suggests they use the ship's nuclear fuel source as well, which will leave the Virgil powerless. Keyes deploys the nuclear core in the last compartment and detaches it just as the triggered detonations start, and then the core's rotation is restarted. Drifting powerless in the core, Keyes and Childs realize they can use the unobtainium shell to convert the heat and pressure from the wavefront to power the Virgil, and they are able to escape from the Earth's core.
They break through the crust underwater, leaving them safe on the ocean floor, but power and communications are offline. They believe themselves lost underwater but use the remaining power to activate a weak sonar beacon. The beacon attracts a nearby whale pod, and Finch is able to trace their whale songs to locate the Virgil. A week after the mission, Finch unleashes the full details of the mission (including those lost) and of DESTINI to the public via the Internet.