"Z/X Code Reunion" is set in a world where five distinct dimensions, each ruled by a different faction, have collided with Earth. These factions, known as the Black, White, Blue, Red, and Green World, deploy powerful beings called Z/X to battle for dominance. The story centers on Azumi Kagamihara, a high school student who becomes entangled in the conflict after her brother, Akira, mysteriously disappears. Azumi discovers she has the ability to summon a Z/X named Rigel, a powerful entity from the Blue World, and is subsequently enrolled in the Academy, a training ground for Z/X users.

The Academy serves as a hub for young individuals who have formed contracts with Z/X, preparing them to defend Earth from the ongoing inter-dimensional war. Azumi joins a group of students, each paired with their own Z/X, including the reserved and skilled Yuni, the cheerful and determined Chitose, the stoic and disciplined Ayase, and the enigmatic and aloof Sera. Together, they navigate the challenges of training, teamwork, and personal growth while uncovering the deeper mysteries surrounding the Z/X and the factions' true intentions.

As the story progresses, Azumi and her companions face various threats, including rogue Z/X, rival factions, and internal conflicts within the Academy. The narrative explores themes of trust, loyalty, and the consequences of wielding immense power. The group's bond is tested as they confront their own fears and insecurities, all while striving to protect their world and uncover the truth behind Akira's disappearance. The series balances action-packed battles with moments of character development, offering a blend of high-stakes conflict and interpersonal dynamics.