Simon is an orphan boy living contentedly in an underground village, where he works as a digger. One day he finds a small drill while he digs, which he keeps. Shortly thereafter his friend Kamina, who he looks up to as an older brother, entices him and two others to try and break through to the surface with their drills. The attempt fails and the village elder chastise all four, telling them that there is no surface. An earthquake suddenly begins and the villagers all panic, including Simon whose parents died in an earthquake. Only Kamina stands tall and unafraid, yelling that they shouldn't have to spend their entire lives scared of earthquakes.
Kamina is chained up in prison overnight by the village elder, and Simon continues to dig. He eventually uncovers a face that seems to resonate with the drill he found earlier; he attempts to break Kamina out of jail to show him, but the two are caught. The village elder begins to beat Kamina but then something breaks through from the surface-- a strange being that looks like a giant animal skull. Kamina snatches the elder's sword to fight it, but is interrupted when a buxom redhead with a sniper rifle appears.
The girl shoots at the creature and is then hit on by Kamina, and Simon digs all three to safety, taking them to the strange thing he found. He eventually works out that his drill functions as a key and he gets the face, which is actually a small mech, to work. Kamina names the mech the Lagann, and Simon manages to defeat the creature (known as a Ganmen, according to the girl) with the help of his companions.
The force of the final blast shoots all three of them up to the surface, where the girl introduces herself as Yoko. Just as they're ready for a break, two more ganmen show up.