A woman named Yuki is attacked by the Lanpyris Worm and impersonated, but she survives, leaving two Yukis running around, but one is swiftly captured and imprisoned. Tensions increase between Souji & Arata, who is quickly falling out of favor with ZECT, as Souji sets the stage for the two Yukis to meet face to face again, kicking off a fight at an amusement park...

Arata must face the difficult truth about who his younger brother really is. Souji confronts Arata, telling him that he will defeat the Worms, no matter who they are. In the end, Arata is left with the toughest choice of his life, as the rain begins to pour…