Yuki Shinohara awakes in Tenjin/Heavenly Host and finds his briefcase on the ground next to him. With inexplicable hallucinations of Seiko's and Miyu's deaths made fresh in his mind, the former child soldier of a crossdresser opens up the briefcase, retrieving from within it his MP5K plus ammo for it.
Yuki proceeds to search Tenjin as he comes across corpses of various students from Kisaragi Academy and other schools. He collects the name tags of each deceased student to bring back as confirmation of their ultimate fates before running into a student from Paulina Academy named Naho Saenoki.
At first, Miss Saenoki mistakes Yuki for the deceased Miyu, which prompts our trappy protagonist if the bespectacled girl knows of his twin 'sister'. Naho replies that she doesn't know 'her' personally, but does know where 'she' died. She points out how to get to the room in question, with Yuki-kun thanking her for the info. Before they part ways, Yuki asks "Why do you come with me? I can protect you with my gun." Naho declines the offer, stating she "Has something else to take care of."
Boss Fight: Unidentified Terrorists?
Shortly after parting ways with Naho, Miyu-chan's heterosexual twin brother finds himself ambushed by a mysterious group of masked men armed with AK-103s, Makaraovs, and PKMs. Yuki recognizes them as members of 'The New Humanity Movement'--the group that kidnapped and turned him into a child soldier--brainwashing him into believing that fighting under their banner would allow him to 'protect what was dear to his heart'. The fight takes place in a length of hallway with various classrooms, with Yuki forced to take them out--either non-lethally or lethally. This fight leaves the second-eldest Shinohara sibling to wonder how his captors and former superiors managed to find him here, how they even got here, and why they opened fire on him.
Following the battle, the crossdressing child soldier ventures alone to a certain medical room in Tenjin. It's here that Yuki Shinohara comes across the severed head and decapitated corpse of his identical twin 'sister', Miyu Shinohara. This triggers one of the fem-boy's recurring nightmares where he is forced to helplessly watch Miyu-chan get torn apart all the way through and from the inside-out before being decapitated at the mouth by tentacles. Upon this nightmare's conclusion, we see poor Yuki-kun on his knees and breaking down in tears as he hugs Miyu-chan's severed head in his arms--blaming himself for "not being there when 'she' (Miyu) needed him most".
The trappy child soldier then hears the sound of approaching footsteps as he puts down Miyu's head and covers both head and body with a nearby bedsheet. Turning around, Yuki points the Deagle in his left hand in the direction of said footsteps. He's shocked to find himself looking at Naomi Nakashima, who was transformed into 'The Girl In Red', albeit a reluctant one. This triggers another flashback, where we see Naomi trying to free Seiko after the former tried to hang her, but from Yuki's point of view, it looked like Naomi tried to kill Seiko-chan. Believing what he saw, Yuki Shinohara accuses Naomi for murdering his older sister, and via the combination of his traumatic child soldier experience, his guilt for 'not protecting Miyu when 'she' needed him most', and said latest revelation, he attacks.
Boss Fight: The Girl In Red (Naomi Nakashima; 1st Encounter)
Throughout this fight, Naomi will try to summon tentacle traps to shield herself from Yuki's shots. As such, defeating the reluctant Naomi will require Yuki to use CQC for a non-lethal takedown. Naomi will engage in CQC as well but is easily countered due to Yuki's combat experience and The Girl In Red's reluctance to fight her close friend.
Following this, we see Naomi flat on her butt, trying to inch away from the revenge-obsessed Yuki. She continues to plead that it was an accident and even attempts to pacify her former crossdressing friend by confessing her love for him. This ends up being fruitless as Yuki-kun gets ready to put a .50 AE round in the forehead of his former tomboyish friend. Naomi, afraid for her life, summons tentacles to restrain him, only to accidentally cause two of the tentacles to impale Yuki through the back--just below the rib cage.
Naomi watches in horror as her once-close friend is lifted up off the ground by the same tentacles while a third tentacle tears his right arm off at the shoulder and a fourth and fifth restrain his legs by the ankles, spreading them apart. Yuki Shinohara screams in extreme pain as a sixth tentacle restrains his left arm by the wrist. The new Girl In Red tries to make the tentacles stop, only to find Yuki still pointing the gun in his left hand at her face. The mortally wounded wholesome crossdresser curses Naomi and declares he'll 'take her to hell with him'--even as a seventh tentacle pierces through the back of his shimapan and stabs his intestines out through his rear-end. Upon ripping them, along with his heart (inexplicably) out of his ass, Yuki manages to fire one last shot, which robs Naomi Nakashima of her right eye.
The Prologue ends with Naomi Nakashima, tearfully cradling the corpse of Yuki Shinohara in her arms. She repeatedly begs her lifeless friend for forgiveness before breaking down on his chest--all while the elder of the Shinohara Twins' left eye stares up into the ceiling, looking completely devoid of life.