In a world overseen by the Time-Space Administration Bureau, an organization which polices over worlds and the use of magic to ensure peace across the universe, three fateful mages are born; Nanoha Takamachi, Fate Testarossa, and Hayate Yagami. After a long, hard struggle, the first two have become close friends, putting a stop to the incident that would come to be known as the Jewel Seeds Incident. Not even a few months later, however, another crisis breaks out as the Book of Darkness, a powerful Lost Logia from ages past, took hold of the third mage, spawning bodyguards, the Wolkenritter, and its avatar, Reinforce, to collect Linker Cores and fill its pages.
As the book neared completion and awakened in a berserk state, Hayate, taking command of the Wolkenritter, Fate and Nanoha, alongside officials from the TSAB, notably Yuuno and Chrono, managed to fight off and destroy the Book of Darkness' defense program, freeing the Wolkenritter and Hayate from its curses. Following this, Reinforce, still alive, requested of Hayate and the others to destroy her as well, so that the Book of Darkness' true programming could not awaken again. Hayate refused, and in this moment of weakness, the book managed to unleash something unexpected: it created a new group of knights for itself, dark, twisted copies of the three powerful mages standing before it. Material-S, Material-L and Material-D fought the gathered heroes, and forcing them to retreat, took the Book of Darkness to withdraw as well, off to another world to recover.
On this new world, the Materials lead dual lives; as normal little girls, they manage to avoid the TSAB's watchful eyes and live a fairly normal life. As servants of the book, however, they ruthlessly hunt down mages for their Linker Cores, a metaphysical organ allowing the use of magic, so that they can sustain the Book of Darkness' existence. With the Multiverse now in sight, the Materials are about to discover a whole new array of possibilities, and many, many more Linker Cores to harvest.