Thirty-five years after the demon emperor Arago was sealed away, the world has largely forgotten the terror he once brought to the human realm. That fragile peace is shattered when the ancient seal weakens, allowing a new demonic army led by the evil emperor Ramaga to invade the mortal world once more. As black clouds consume the skies over modern-day Shinjuku and demon soldiers pour through, a new generation of five young warriors is called upon to don mystical suits of armor known as Yoroi and become the Samurai Troopers, humanity's last line of defense.

The story follows these five teenagers, each bonded to an armor representing a distinct virtue and elemental power. Gai, a former member of Ramaga's own Ten Braves, becomes the wielder of the Shakunetsu no Yoroi, the Burning Armor associated with fire. Initially an anti-hero with violent tendencies, he must learn to control his darker impulses and grow into his role as a true hero. Musashi Hojo, a kind-hearted boy who was the sole survivor of his previous, corrupt trooper team, inherits the water-based Suiren no Yoroi, or Water Lily Armor, which grants defensive and healing abilities. The team is rounded out by Kaito Uesugi, the otaku wielder of the sky-manipulating Soukyuu no Yoroi; Yamato Hojo, Musashi's older brother who commands the earth-based strength of the Kouya no Yoroi; and Shion Ishida, the strategic leader whose Senkou no Yoroi harnesses the power of light and lightning to purify darkness.

The narrative begins with the demonic invasion and the formation of the new Troopers, who are initially supported by the Defense Special Task Force (DST), a government organization that also manages a separate, ineffective team of publicity-focused troopers. A key figure is Ryusei Oda, a scarred DST recruit who trains the new generation, and the returning character Nasti Yagyu from the original series, who now serves as the DST's director and a mentor to the young warriors. Researcher Mirei Aragaki also provides crucial technological support for the team's armor evolutions. The early episodes establish a darker and edgier tone than its predecessor, with graphic violence and morally complex situations, such as when Gai brutally murders Musashi's corrupt former teammates as karmic retribution for their selfishness.

A major narrative arc unfolds when Ryusei is shot by a magical bullet, losing his powers and later being possessed by the demon emperor Ramaga himself. His apparent loss leaves the Troopers fractured and grieving. Episode six serves as a soft reboot for the series, with Shion stepping up as the team's new driving force while using Ryusei's notes as a guide. Meanwhile, Gai undergoes a rigorous training arc fueled by posthumous mentorship from Ryusei, allowing him to confront his violent past and prejudices. Ramaga grants the Troopers a seven-day ultimatum, leading to a tense period of preparation. The arc builds towards a climactic confrontation where the heroes must unite their newfound strength and resolve to stop Ramaga, facing personal sacrifices and the true cost of their victory as they battle to prevent the demon world from consuming Tokyo entirely.