The story opens some time after the end of the American Civil War. The Baltimore Gun Club, a society dedicated to the design of weapons of all kinds (especially cannons), comes together when Impey Barbicane, its president, calls them to support his latest idea.

During the American Civil War, five Northern risoners of war escape during the Siege of Richmond, Virginia, by hijacking a hydrogen-filled observation balloon.

The story starts with a comet called Gallia, that touches the Earth in its flight and collects a few small chunks of it. The disaster occurs on January 1 of the year 188x in the area around Gibraltar.

During an expedition to Iceland, professor Trevor Anderson (Brendan Fraser), his nephew Sean (Josh Hutcherson) and their guide, Hannah (Anita Briem), get trapped in a cavern. As they follow their only escape route deeper and deeper below the Earth's surface, they pass through strange places and encounter incredible creatures, including dinosaurs.