With its armies sweeping across the continent, the Empire seems unstoppable. After securing victory over the remnants of the Republic's army, the Empire's ultimate victory is finally within reach. However, dark clouds are gathering in the East. The communist-led Russy Federation is mustering troops on its western border, preparing to enter the war. Supported by a detachment of Allied volunteer magicians—among whom is Mary Sioux, the daughter of a soldier killed by Tanya Degurechaff—the Federation is determined to spread the communist creed and bring the Empire to its knees. Meanwhile, Tanya and her battalion return to the imperial capital from the southern front. Upon their arrival, they are tasked with investigating troop movements on the border with the Federation. Any escalation of violence at this point may lead to new conflicts, plunging the world into a devastating global war. Will the Empire eventually emerge victorious from its struggle, or will it crumble in the face of superior enemies and radically different ideologies?

In the Kingdom of Midland, a mercenary named Guts wanders the land, preferring a life of conflict over a life of peace. Despite the odds never being in his favor, he is an unstoppable force that overcomes every opponent, wielding a massive sword larger than himself. One day, Griffith, the mysterious leader of the mercenary group Band of the Hawk, witnesses the warrior's battle prowess and invites the wandering swordsman to join his squadron. Rejecting the offer, Guts challenges Griffith to a duel—and, much to the former's surprise, is subsequently defeated and forced to join. Now, Guts must fight alongside Griffith and his crew to help Midland defeat the Empire of Chuder. However, Griffith seems to harbor ulterior motives, desiring something much larger than just settling the war...

In the year 2063, space travel is feasible and commercially available. As the cheerful Aries Spring arrives at the spaceport to attend a camp on the distant planet McPa, her purse is suddenly snatched by a reckless thief. Luckily, the athletic Kanata Hoshijima is able to retrieve it for her, and Aries soon discovers that he is among the group of teenagers who will be traveling with her on the excursion as team B-5. Upon arriving at their campsite, the group's trip takes a turn for the worse when a strange sphere of black light sucks them into the vast reaches of outer space. Stranded with seemingly no hope, they find an abandoned ship nearby that provides them with the means to return home. However, they soon discover that they are not as close to their campsite as they initially thought, but are in fact thousands of light-years away from home. With this realization, the nine members must cautiously manage their resources, maintain their strength, and unite as one to conquer the darkness of space together. While the reason behind their trip's sudden obstruction remains unknown, they nevertheless embark on the treacherous voyage back home aboard their new ship, the Astra.

The Celestial Records speak of the existence of the Seraphim, a race of divine beings who give blessings to humanity and are offered prayers by them in return. Those who are anointed with the ability to interact with these spirits are known as Shepherds. Hailed as heroes for their prompt appearances in times of crisis, while also being feared for their power, the Shepherds are imprinted in common folklore along with the Seraphim. Sorey is a young human who has spent his entire life living in harmony alongside the Seraphim in the village of Elysia. Fascinated by the myths of the Celestial Records, he explores some nearby ruins with Mikleo—his childhood Seraphim companion—hoping to enlighten himself about the Seraphims' history with mankind. Unfortunately, they become trapped in the depths of the historical site during their investigation. While searching for an exit, they come across a mysterious girl who desperately seeks the help of a Shepherd to save the world, which is on the brink of being consumed by darkness. Despite Mikleo's warning about making contact with other humans, Sorey decides to help the stranger, which unknowingly leads him closer to the dream of peaceful coexistence between man and Seraphim.