Kazuma is a Native Alter user who makes his living as a mercenary so that he and his close friend, Kanami Yuta, can live together. Kazuma's friend Kunihiko Kimishima gives him a mission to defeat another Native Alter user. However, a man known as Ryuho from HOLY captures Kazuma in the aftermath; during this, Ryuho tries to interrogate Kazuma about an unknown Alter user (later dubbed Crystal) who killed his mother and dog. After managing to break free of his bonds, Kazuma uses a female HOLY agent named Mimori Kiryu as a hostage and manages to escape the facility and make it back to his house. However, HOLY then arrives and proceeds to capture many Native Alter users, during which Kazuma meets Crystal in a forest, and the two proceed to fight, after which his Alter receives a power-up. Later on, it's revealed that the Great Uprising was caused by a similar event in a parallel universe where all creatures are independent, thinking Alters. Kazuma then goes on a rampage against HOLY after Kimishima dies while helping him during one of his fights, which leads to him and Ryuho fighting again; however, during their battle, they end up opening a gateway to the parallel universe, causing another uprising and attracting the attention of the Mainland government. Both Kazuma and Ryuho are believed to have died following this event, when, in actually, the former goes into hiding in an underground fighting circuit whilst the latter ends up suffering from amnesia. With help from an old friend, a HOLY member known as Straight Cougar, Kazuma recovers his will to protect Kanami, who hasn't stopped looking for him. Meanwhile, Ryuho manages to recover his lost memories whilst protecting Natives from HOLY agents, ultimately leading to him becoming an ally of Kazuma. The Mainland sends one of its best agents, Kyouji Mujo, to the Lost Ground in an attempt to exploit the power of the parallel universe for economic gain. However, Mujo develops delusions of grandeur after becoming the de facto head of the Lost Ground government and absorbing the Crystal entity from "the other side" to add to his already formidable Alter power. Both he and Crystal are defeated by the separate efforts of Kazuma and Ryuho, respectively, as both increase their Alter powers by taking energy from the parallel world. The Mainland once again attempts to exert control over the Lost Ground by sending in a fleet of refined Alter users under their control, only for all of them to be defeated by Kazuma and Ryuho. Following the defeat of the Mainland forces, Kazuma and Ryuho decide to engage in one final battle to finally settle their rivalry. As one of them is about to declare victory, the screen fades to white. In an epilogue, taking place years later, they remain the protectors of the Lost Ground and defend it from Mainland invaders; meanwhile, an older Kanami awaits their return, Dou wtach and enjoy.
