To defend against Nightfly O'Notes, invaders from another world, mankind has organized the five-man fighting team "Scar-red Rider XechS." However, one of the Riders, Yosuke, is saddled with a serious problem.
When Akira, the new instructor-in-charge, assumes her post, the Scar-red Riders' leader, Takt, finds himself unable to trust her. Friction arises between Takt and Yosuke. During all the discord, there is an enemy attack.
After being hurt in battle, Hiro's physical injuries heal, but as he grows more distant from the group, it becomes obvious that some mental wounds still remain. Akira tries to get the Riders to focus on their teamwork.
To shoot a promotional video for the Scar-red Riders, the group goes to the seaside town of Shonan. While away from their usual fighting, Kazuki tries to write a song, while Takt discovers an unexpected facet to Akira's personality.
Hijiri, a transfer student with a flirty attitude, makes sport of the other Riders. When Hijiri approaches Akira, Yosuke becomes mindful of her. While fighting an enemy with odd motives, Kazuki enacts a surprising plan.
As autumn sets in, Ryukyu LAG is caught up in the excitement of the school festival. The Riders practice for their first live concert and work to promote it. Akira and Hako strengthen their friendship. LAG gets an unusual visitor.
A powerful Nightfly O'Note attack on Ryukyu LAG headquarters leaves the Scar-red Riders in a precarious position. Hijiri begs Epiphone to undergo resonance with him so that he can protect Akira.
The Riders, the Substances, and Akira enjoy themselves while preparing for a Christmas party. Troubled by past memories, Hako suffers an identity crisis. A major conspiracy within the government goes into action.
Akira is taken to Tokyo LAG, where Hako has her own agenda concerning her. Grunbach launches an all-out invasion of the capital of Tokyo. Okazaki, anticipating such an attack, initiates her plan to counter the threat.
The war with the Nightfly O'Notes is not yet over, but having lost their friends, the grieving Akira, Yosuke, and other Scar-red Riders have a difficult time navigating the healing process to get back on their feet.
A new foe appears before Akira and the Scar-red Riders. Despite the shock of seeing this new foe, the group returns to Ryukyu LAG to mount a last-ditch effort. While Akira is getting ready, a familiar face shows up.
With the red moon shining overhead, the end of the world begins. As the Scar-red Riders take to the battlefield, Yosuke and Takt face off, and Akira realizes the reasons why they have all been fighting for so long.
