Thirty-five years after the defeat of the demon emperor Arago, the seal holding back the netherworld has weakened, allowing a new wave of demonic forces to invade the human realm. Led by the evil emperor Ramaga, these hordes of demon soldiers break free and begin their assault on modern-day Shinjuku, plunging the city into chaos as black clouds and supernatural disruptions signal the return of an ancient evil. In response, five young warriors rise to defend humanity, each chosen to wear a mystical yoroi armor that grants them incredible power drawn from virtues such as benevolence, justice, courtesy, wisdom, and trust.

These five Samurai Troopers are a new generation of heroes, distinct from the legendary warriors who fought Arago decades earlier. Gai wears the Shakunetsu no Yoroi, the Burning Armor, and commands fire-based abilities centered on intense heat and scorching attacks. Kaito Uesugi dons the Soukyuu no Yoroi, the Azure Sky Armor, granting him aerial agility and wind manipulation for high-mobility reconnaissance and assault. Musashi Houjou, from the Forest of Truth orphanage, equips the Suiren no Yoroi, the Water Lily Armor, which provides water-themed defensive barriers and healing waves. His adoptive older brother Yamato Houjou wears the Kouya no Yoroi, the Wilderness Armor, bestowing earth-infused strength and endurance that allows him to manipulate terrain and serve as an emotional anchor for the team. Shion Ishida serves as the group's leader, commanding the Senkou no Yoroi, the Flashing Light Armor, which uses light and lightning purification mechanics to dispel darkness and coordinate synchronized assaults.

The conflict deepens as the government establishes a Defense Special Task Force to manage the new Troopers, though these young warriors are initially treated more as ineffective publicity symbols than genuine heroes. The official team struggles under the weight of expectations, while figures like Gai and Musashi form fresh alliances rooted in authentic heroic ideals rather than media appearances. Mirei Aragaki, a tech expert and assistant commander within the DST, provides crucial reconnaissance and technological support, helping the Troopers enhance their armors and counter demonic threats. Meanwhile, the antagonists include Ramaga's Ten Braves, a host of demons with dark yoroi counterparts that mirror the protagonists' armors, each engaging in brutal battles that emphasize the series' darker and more violent tone compared to the original. These demonic forces display unsettling behaviors, such as singing 1980s pop songs while slaughtering civilians, reflecting how the demon world has remained frozen in the decade of its original attack.

The narrative unfolds across a twelve-episode first season, beginning with the breaking of the ancient seal and the emergence of demon soldiers in Tokyo. Early episodes focus on the formation of the new Trooper team, as characters like Kaito lose loved ones to the invasion and tensions rise during virtual training sessions. The plot escalates as Ramaga issues an ultimatum, forcing the Troopers to confront their weaknesses and risk everything to rescue captured allies like Mirei. The Troopers must seek out three sacred treasures to gain the power needed to enter Ramaga's castle, leading to revelations about the demon emperor's plans and a final confrontation that tests their unity and resolve. The series introduces Shinden evolutions of the yoroi armors, which allow for spiritual energy fusion and enhanced combat abilities during battles against demonic entities, representing a key innovation that distinguishes this sequel from the original 1988 series.