On the surface, the remnants of humanity endure attacks by humanoid Beastmen piloting powerful robots known as Gunmen. Far below, Simon and Kamina have grown up in a village where the world above is only a legend. Timid Simon has few ambitions, while the reckless Kamina longs to make a name for himself.
During an excavation, Simon uncovers a mysterious key that activates an ancient war machine, which the pair names Lagann. When an attack comes from the surface, they use it to fight back with help from Yoko Littner, a heavily armed traveler from above. The battle leaves the sky visible, and the two head out with Yoko to explore the wastelands. Joining other survivors against the Beastmen, they struggle to reclaim the surface while gradually uncovering a mystery of galactic proportions.