In the year 3990, the immortal Oldna Poseidal rules Pentagona, a war-torn solar system of five planets. Daba Myroad is a survivor of the Yaman Clan, just one of numerous native societies nearly wiped out by the tyrant. Living on the remote planet Koam with his friend Mirao Kyao, Daba possesses L-Gaim, a humanoid mecha known commonly as a "Heavy Metal" and the last known relic of the Yaman Clan. The pair befriend Fanneria Amu, an aspiring actress, and Lilith Fau, the last surviving fairy in Pentagona while on the run from a band of thieves attempting to steal L-Gaim. Daba promises to fulfill the dying wish of one of the thieves hunting him—an honorable act that leads him to the powerful merchant Amandara Kamandara. With their mission in sight, the ragtag group will face powerful adversaries and become entangled in a rebellion against Poseidal's reign.

A side story taking place somewhere before the second half of the series, prior to Daba acquiring the L-Gaim Mk-II. Daba's comrade Leccee is captured by Poseidal's forces, and Daba and his rebels attempt to save her.

Decades into the future, humanity is under siege by an alien race known as the Novas. These inhuman beings leave devastation in their wake whenever they appear, with the efforts to stave them off becoming known as Nova Clashes. Young women known as "Pandoras" and young men known as "Limiters" are implanted with stigmata to give them superhuman powers and are trained in military academies, where they must learn to work together if humanity is to have a chance of surviving. Freezing tells the story of Kazuya Aoi as he sets out for his first day at the West Genetics military academy, right when a battle royale is being undertaken by the Pandoras. It is here that he mistakes Satellizer el Bridget—a powerful Pandora known as the "Untouchable Queen"—as his deceased sister and embraces her. Though he costs her the match, she finds that his touch doesn't drive her away and decides to take him as her Limiter. The only question is whether or not their partnership can survive the machinations of their upperclassmen and the impending battle with the Novas…

Ever since the 10th NOVA clash, the Chevalier had concluded that the NOVA have been appearing at a steadier rate and they are losing more Pandoras than they can produce. Their solution is the E-Pandora Project which involves normal humans being given the power to become Pandoras. Inviting Pandora from around the world to their Alaskan base witness the unveiling of their new project, Satellizer, Kazuya and Rana are among those who have been summoned. However, as time goes the E-Pandora Project starts to become fishier and the Pandoras start to grow more and more concerned...