Following Armageddon, an apocalyptic war, mankind faces yet another menace: vampires. The continuous confrontations between the races have split the world into separate factions. The race of vampires, Methuselah, are affiliated with the New Human Empire; whereas the humans, deemed Terrans by the vampires, make up the Vatican Papal State. Furthermore, extremist groups like the Rosenkreuz Order strive to rekindle a war, despite the factions' attempts to avoid direct conflict. To combat terrorist organizations, the Vatican has implemented the AX unit. Led by Cardinal Caterina Sforza, the AX agents investigate vampire-related disturbances with hopes that the Terrans and the Methuselah will one day achieve a peaceful coexistence. Amongst the AX unit is priest Abel Nightroad—a seemingly disoriented but gentle-hearted fellow, and a fierce vampire slayer on the battlefield. Joining the unit as his partner is a new agent, Sister Esther Blanchett, a brave and gentle young nun troubled with a tragic past. As the two grow closer, they begin to uncover signs of malicious schemes and dark forces working in the shadows. But the path they walk is riddled with misfortune that might just force them to confront the memories that plague their hearts.

In the distant future, because of an interplanetary war that had continued on for centuries, civilizations were ruined. Human beings have lost everything, and only 1/5th of the population survived. A strange breed of humans, ''The Third'' is said to have appeared just after the war. They possess a third eye, as their name suggests, that appear as oval-shaped red pupils called "space eyes'' over their conventional two eyes. Using them, they can control computer systems and so on, and as such, rule the world by their superior power over technology. In this world, there is a young woman named Honoka; she is a "jack-of-all-trades" sellsword, and she accepts any job except murder. One day, she happens to find and rescue a young man named Ikus in the desert. Entering his world, and accepting a job from him, the adventure begins for Honoka and Ikus.

Ever since his powers awakened, Tenchi Masaki has attracted the attention of many powerful galactic beings, including the mysterious Lady Takami who dispatches her best warrior, Z, to observe him. Though he is under strict orders not to harm Tenchi, Z has no intention of playing by the rules and begins plotting his demise. Meanwhile, on Earth, Tenchi tries to piece together more information about his family and the universe. But as usual, his life won't be getting any easier, as his entire household enters a state of panic when Noike Kamiki Jurai—a woman claiming to be Tenchi’s fiancée—shows up out of the blue. [Written by MAL Rewrite]

Six months have passed since the victorious Battle of Britannia and the reclamation of Gallia from Neuroi invaders. Yoshika Miyafuji, member of the famed 501st Joint Fighter Wing, has come back home to Fuso and graduated from middle school. However, her fight is far from over. She receives a letter supposedly sent by her long-deceased father, containing blueprints of a state-of-the-art Striker Unit he had been working on before his death. The Unit, designed specifically for Yoshika, might be capable of harnessing her extraordinary magical powers. Meanwhile, a new threat in Europe is rising. A Neuroi nest of an unprecedented size and might has appeared over Venezia, wiping out local Witch forces and instantly swallowing the northern part of the country. To make matters worse, a newly spotted humanoid type of Neuroi is attempting to come into contact with humans. Yoshika, incapable of abandoning her friends on the front lines, must once again venture to the war-torn continent. [Written by MAL Rewrite]