Six months after the events of Ginga: The Last Wars, the young warrior Orion has gone missing while trying to bring news of his brother Sirius's death to his mother. The soldiers of the Ou army grow concerned and set out to find him. During their search, they encounter a new and terrifying threat: the Aka-Ari, or Red Ants, a massive army of rogue dogs led by three colossal Tibetan Mastiff brothers named Wanwan, Shuou, and Beniou. Believing the Ou army was wiped out by bears, this cannibalistic horde has been sweeping across Japan, destroying anyone who stands in their way and murdering the puppies of Ou soldiers, including those of heroes Jerome and Lydia.

Meanwhile, the depressed and weary Orion is pulled from the ocean and brought to a mysterious old dog living in the wilderness. This elder is Noah, a gentle soul who cares for lost puppies with the help of his companions, Buna and Kogomi. Although Noah does not recognize Orion, seeing the young Akita triggers powerful flashbacks to a violent past he cannot fully remember. Noah is eventually confronted by one of the Aka-Ari commanders, Shou, who nearly kills him. As Noah teeters on the edge of death, he has an out-of-body experience and his memory returns in a flood. He realizes he is not simply Noah, but Hyena, a former soldier of Riki's original Ou army and a former minion of the villain Sniper. Hyena had survived being swept away in a river years ago, only to be rescued by a human who gave him a new name and a new life. After his owner later perished, Hyena, now fully embracing the identity of Noah, dedicated himself to protecting the innocent.

With his memory restored, Noah receives a dire prophetic vision of a great disaster that will soon befall all dogs. Just as Orion reunites the Ou army to confront the Aka-Ari leadership, Noah's prophecy comes true in a catastrophic fashion. A meteor shower slams into the region, causing a massive tsunami, volcanic eruptions, and widespread chaos. The ensuing natural disaster interrupts the battle, forcing both the Ou dogs and the surviving Aka-Ari leaders to seek shelter in an abandoned mine.

The meteor strike also brings a bizarre new element to the conflict: parasitic alien thread worms. Wanwan is killed by human military forces but is revived by these worms, becoming an infected, nearly invincible monster. In turn, Wanwan infects and kills his own brother, Beniou. Realizing that the worms are vulnerable to salt water, Noah and a mysteriously revived Sirius use their combined spiritual power to launch the infected Wanwan and Beniou into space before plunging them into the ocean, where the worms and the two brothers disintegrate for good. With the Aka-Ari and the alien threat neutralized, the Ou army begins to rebuild, bringing the story to a close as Noah continues his life as a guardian of the helpless.