In Universal Century 0079, near the end of the One Year War between the Earth Federation and the Principality of Zeon, the space colony of Side 4, known as Moore, lies in ruins. The debris field of destroyed colonies and warships has become a treacherous shoal zone, where constant collisions of electrified wreckage create dangerous lightning flashes, earning it the name the Thunderbolt Sector. This treacherous battlefield is where the story begins, as the Earth Federation forces, specifically the Moore Brotherhood unit composed of survivors from Side 4, fight to reclaim their homeland from the Zeon forces.

The central conflict revolves around two ace pilots on opposite sides who recognize each other as destined rivals. Io Fleming is a reckless and rebellious Federation pilot who uses jazz music to drown out the horrors of battle. He pilots the Moore Brotherhoods mobile suits and eventually takes control of a powerful prototype, the Full Armor Gundam. His driving force is a desire to feel alive in combat, hating the idea of being tied down by his homeland or family history. On the opposing side is Daryl Lorenz, a calm and skilled sniper for Zeons Living Dead Division, a unit composed of soldiers who have lost limbs in combat and use prosthetic replacements. Daryl, who has already lost his legs, fights to protect his comrades and finds solace in pop music. When Io hijacks an enemy mobile suit and comes face-to-face with Daryl early in the conflict, they each realize they are fated to be each other's ultimate adversary.

The narrative arc of the first season follows the escalating war between the Moore Brotherhood and the Living Dead Division within the Thunderbolt Sector. As Io demonstrates devastating effectiveness in the Full Armor Gundam, the Zeon forces become desperate to counter this new threat. Karla Mitchum, a researcher in the Living Dead Division who develops prosthetic limbs, pushes forward the Reuse P Device project, which allows a pilot to control a mobile suit with their entire nervous system. To become the perfect pilot for the experimental Psycho Zaku, Daryl willingly sacrifices his remaining organic limbs, having his right hand amputated to fully interface with the machine. The situation becomes even more grim when the Moore Brotherhood receives reinforcements in the form of inexperienced young teenage pilots, leading to a massacre when Io leads them into battle against the Zeon defenses. The climax of the season is a brutal final showdown between Io in the Full Armor Gundam and Daryl in the Psycho Zaku, which leaves both mobile suits heavily damaged. A Zeon reinforcement fleet arrives, capturing Io and the surviving Federation forces while rescuing the remaining Living Dead members.

A sequel season continues the story eight months after the end of the One Year War. The Earth Federation now battles Zeon remnants on Earth, and a new faction called the South Seas Alliance has emerged, possessing the Psycho Zaku technology. Io Fleming is assigned to pilot a new prototype, the Atlas Gundam, on a mission to track down and destroy the Psycho Zaku before the technology can be mass-produced. Meanwhile, Daryl Lorenz has gone to Earth to join the Zeon remnants and is tasked with gathering intelligence on the Psycho Zaku. The conflict expands from the depths of the Antarctic Ocean to the jungles of Southeast Asia, as both pilots are drawn back into their fateful rivalry and the chaos of the post-war era. The series explores the brutal psychological toll of war, the sacrifices soldiers make to survive, and the thin line between duty and obsession.