A young boy named Shu Matsutani, a passionate kendo student, sees a strange girl with blue hair sitting alone on a factory smokestack at sunset. When he tries to protect the girl, Lala-Ru, from mysterious abductors piloting dragon-like mechanical transports, he is accidentally transported to another world. This new reality is a desolate, post-apocalyptic wasteland dominated by a swollen red sun in a dark sky, where water is the most precious and scarce resource.

Shu is quickly captured and imprisoned aboard a massive, mobile fortress called Hellywood, the stronghold of a deranged and childlike dictator named Hamdo. Hamdo obsessively seeks Lala-Ru because she possesses a pendant that contains a vast reservoir of water, which she can control with her will. In the fortress's brutal prison, Shu meets Sara, an American girl who was kidnapped by mistake. She is forced into the army's quarters and suffers repeated sexual assault.

To survive, Shu is conscripted into Hamdo's army, a unit of child soldiers led by a boy named Nabuca. These children are trained to raid villages, kidnap women for breeding, and capture orphaned boys to replenish their own dwindling ranks. Shu, armed only with his wooden training sword and his unwavering belief in non-violence and the inherent good in people, endures relentless torture, hunger, and the horrors of war. He struggles to protect the emotionally detached and nearly immortal Lala-Ru, who has grown disillusioned with humanity over her long life, while trying to maintain his own humanity in the face of senseless brutality.

The narrative follows Shu as he is moved from Hellywood to the resistance stronghold of Zari-Bars, where a tough but nurturing woman named Sis cares for war orphans. The story reaches its climax when Hamdo's paranoia and desperation drive him to launch a full-scale attack on Zari-Bars to reclaim Lala-Ru. In the ensuing chaos, characters like the conflicted child soldier Nabuca meet tragic ends. Ultimately, Lala-Ru uses the full power of her pendant, unleashing a catastrophic flood that destroys Hellywood and brings water back to the barren world. Hamdo meets his end, drowning in the flood during a complete mental breakdown. In the aftermath, Abelia, Hamdo’s devoted but weary commander, finally abandons his cause and helps send Shu back to his own world. Shu returns to his home at the exact moment he left, forever changed by the war he witnessed and the friends he lost.