Simon and Kamina grow up in a deep subterranean village, hidden from the legendary surface world. Kamina is a wild, impulsive rebel determined to carve out his own legend, while Simon is a shy boy without any real dreams. While digging through the earth one day, Simon uncovers a strange object that proves to be the activation key for an ancient war machine, which the two name Lagann. With their newfound weapon, Simon and Kamina repel a sudden assault from the surface, aided by Yoko Littner—a fierce redhead with a large gun who roams the world above.
After the fight, the sky becomes visible for the first time, inspiring Simon and Kamina to embark on a journey with Yoko across the barren surface. They soon join the struggle against the "Beastmen," humanoid monsters that torment what remains of humanity using powerful mecha called "Gunmen." Despite encountering difficulties and losses, the trio courageously battles these foes alongside other survivors to take back the surface, gradually uncovering a mystery that spans the entire galaxy.