"Reideen" centers around Junki Saiga, a high school student who discovers his connection to an ancient, colossal robot named Reideen after his father's mysterious disappearance. The narrative begins with Junki visiting the site of an archaeological dig where his father was last seen. During this visit, a massive alien creature attacks, and Junki is drawn to a glowing artifact that awakens Reideen. The robot, which has lain dormant for centuries, bonds with Junki, granting him the ability to pilot it and defend Earth against the alien threat.

The series unfolds as Junki learns to harness Reideen's powers while grappling with the responsibilities of being its pilot. The alien invaders, known as the "Messengers," are relentless in their attacks, each encounter revealing more about their origins and motives. Junki's journey is marked by personal growth, as he navigates the challenges of balancing his ordinary life with the extraordinary demands of piloting Reideen. Along the way, he forms alliances with other characters, including his childhood friend Akira Midorino and a mysterious girl named Rikka Hoshino, who possesses knowledge about Reideen and the Messengers.

As the story progresses, the true nature of Reideen and its connection to Junki's family history is gradually uncovered. The robot is revealed to be a relic of an ancient civilization, designed to combat the Messengers, who seek to harvest Earth's energy for their own survival. Junki's father, a scientist, had been researching Reideen and its origins, which ultimately led to his disappearance. The series delves into themes of legacy, sacrifice, and the burden of protecting humanity, as Junki confronts the moral and emotional weight of his role.

The plot intensifies with the introduction of rival factions and competing interests, including government agencies and other individuals who seek to control Reideen for their own purposes. Junki must navigate these external pressures while also facing internal struggles, as the bond between him and Reideen grows stronger, revealing new abilities and challenges. The series builds toward a climactic confrontation with the Messengers, where Junki's resolve and the true potential of Reideen are put to the ultimate test.

"Reideen" combines elements of mecha action, science fiction, and personal drama, creating a narrative that explores the intersection of human emotion and technological power. The series maintains a focus on Junki's evolution as a character, his relationships with those around him, and the broader implications of Reideen's existence in a world under siege.