Act 1: Seiko Shinohara Arc
Despite having his heart and bowels essentially torn out of his a**, Yuki Shinohara finds himself awake in a different room, where he finds looking down on him a Girl In Red who resembles a pacified Sachiko Shinozaki. This girl introduces herself as 'Sachiko Two' and informs Yuki Shinohara of her rebuilding him using "various body parts lying around". Yuki-kun then sits up and finds his now-exposed abdominal area wrapped in bandages before rubbing his right shoulder and his chest. He remarks his "right arm and heart don't feel like his own, yet they feel familiar.". Sachiko Two doesn't tell him who gave her these body parts in question to graft onto him, but does reply his digestive system from the stomach all the way down to the 'exit' were repaired through the use of a special serum. On top of that, the clone of the previous Girl In Red adds she was only able to resurrect the fem-boi child soldier because unlike his sisters, Yuki did not end up decapitated.
(Yuki responds to said revelation with the mention of rumors of him being 'decap-proof' having spread like wildfire. He says this came from multiple incidents in which he had taken headshots from rounds that would normally cause a person's head to explode getting lodged in spots before they could reach his brain, along with other incidents where every single blade used to cut his neck had broken--unable to even cut into his throat. Exactly why he keeps surviving from such he doesn't know.)
To his bewilderment, the former child soldier learns the serum Sachiko Two used to fully repair his bowels came from tentacles--specifically her own 'tentacle tails'. She apologizes to Yuki believing the very sight of tentacles reminded him of Miyu Shinohara's death, along with his own just now, which Yuki mercifully lets slide. From this, the two have a conversation in regards how they came to be--Sachiko Two having been created by the original Sachiko Shinozaki to 'protect' the lost souls in Tenjin following the place being sealed by Ayumi near the end of Corpse Party Musume, and Yuki being a former child soldier who accepted a mission by Defense Intelligence HQ to investigate missing persons cases tied to Kisaragi Academy.
The conversation ends with a new friendship having blossomed and Sachiko Two, who then gives Yuki a radio to contact her with in case he needs anything. The two then part ways, but not before the wholesome crossdresser that is Miyu Shinohara's twin brother asks himself if he's developing feelings for the 'tentacle girl' that resurrected him. He's able to sense that he still won't be able to live a normal life and wonders if it's the same case for the girl as well.
Yuki-kun fights his way through more ambushes from New Humanity Movement terrorists (either head-on or stealthily) while evading (or somehow combating) various malevolent spirits in Tenjin/Heavenly Host Elementary. Eventually he runs into the ghost of his older sister, Seiko Shinohara--finding her cornered and interrogated by what appears to be a girly-looking cyborg ninja. This trappy-looking cyborg ninja looks just like Miyu-chan from above the jaw, with his artificial body having a feminine boy shape to it (Read: Think of the girls' uniforms from Horizon In The Middle Of Nowhere and you have what this cyborg ninja's body looks like.)
Boss Fight: Miyu Zwei
Yuki Shinohara confronts the fem-boi cyborg ninja resembling his deceased twin 'sister' and...well, himself, asking him why he attacked Seiko. Miyu Zwei replies his programming does not allow him to disobey direct orders, which would result in his permanent shutdown. He continues by revealing his orders--terminate Yuki Shinohara.
Miyu Zwei, just like any cyborg ninja in the Metal Gear series, is armed with a HF Blade. His hips also mount pincer-like waldo claws that seem to conceal heat blades in their cores, and he also carries what appears to be a left-handed M4A1 Carbine with a Beta C-Mag. This fight is difficult to survive through CQC alone, but regardless of whether Yuki defeats Zwei-kun lethally or non-lethally, the result will be the same: Miyu Zwei will mindlessly ramble about his desire to be free, yet somehow be unable to understand it.
Yuki Shinohara feels the need to kneel down Miyu Zwei and remark "You're...me, aren't you?", which confuses the ghostly Seiko even more. Yuki then fills in his onee-chan over what happened to him since he and their mother, Sayaka Shinohara, disappeared. Seiko Shinohara, the older sister of Yuki, Miyu, and Yuu, in addition to being the secret lover of Naomi Nakashima, is horrified to learn that Yuki was brainwashed into becoming a killing machine. He then asks his eldest sister why Naomi murdered her--only to get silence.
Distraught, Yuki asks his eldest sister repeatedly the same question, with Seiko turning her face away from him, replying "You're...going to kill her?" Still believing Naomi intentionally caused his onee-chan to end up decapitated, Yuki can only think about killing the girl he once loved, but then feels his heart hurt. Seiko clutches her heart at the same time as this, sensing her brother's thoughts in the process. She begs Yuki Shinohara, the equally trappy twin brother of Miyu Shinohara, to spare Naomi with the words "She knew not what she did". Yuki could not respond, but instead radioed Sachiko Two about a cyborg he rendered inoperable. He asks her if she can find a way to 'free' him, which she gets to work on. The two then leave the room in question.
Despite this new rift in their relationship, Seiko would follow Yuki around Tenjin as the latter sought for his pursuers and the reason behind them hunting him down. As they captured terrorist after terrorist, the eldest Shinohara Sibling would learn of the 'Child Soldier Uprising' her eldest brother was involved in. This triggers a flashback of the same Uprising, where we see then-child soldier of a wholesome crossdresser mowing down adult personnel with what looks like a left-handed M134 Minigun rigged to a Jury-Rigged Railgun of sorts back-to-back (This weapon, the Dual Weapons Case, is inspired by the Destroyer used by Chung from Elsword). In the same flashback, we see multiple other boy soldiers dressed as girls and utilizing custom-built armament to lay waste to the very terrorists that brainwashed them in the first place.
Said flashback ends with Yuki tackling Seiko to the ground to save her from being hit by a hail of gunfire that came from outside Tenjin. The two look out the window to find themselves looking at a jet-black Hind D with no markings. However, the former child soldier manages to get a glimpse of the pilot--recognizing the 'boy that looks like Erica Hartmann from Strike Witches' as his former comrade--Master Sergeant Erich Wolfe.
Boss Fight: Hind-D (Master Sergeant Erich Wolfe)
During this fight, Yuki will have the benefit of Seiko Shinohara's ghost form being able to deflect rockets and missiles fired in their direction, but not Autocannon shots. The whole fight takes place on one side of the top floor, with Yuki and Seiko required to move from room to room in order to evade gun strafing and barrages of rockets. The first half of this fight is pure survival, as Yuki has nothing to fight off the Hind in question while Erich angrily questions him about his 'betrayal'--something Yuki denies in an equally angry tone.
This changes when a strange set of tentacles emerge from under one of the cabinets, proceeding to grab Yuki-kun and elevate him off the ground. One tentacle buggers him underneath his shimapan's right legband while two more tentacles each pull out from some black magic portal a pair of PTRS-41 Anti-Tank Rifles. The otokonoko of a former child solider finds himself looking at some sort of 'Magic HUD', which he attributes to the slime being pumped into...yeah. In what Seiko dubs 'Tentacle Sentry Mode', Yuki can fire the PTRS-41s (currently w/unlimited ammo) at the Hind to take it down. Once that happens, Erich curses at the dying chopper to 'Fly~!' before screaming out Yuki's name.
The Hind-D and its trappy pilot plummet into the darkness, and a loud explosion can be heard and felt while Yuki is freed from the strange set of tentacles that actually helped him. (One PTRS-41 is left behind for our trap protagonist to use.)
At this point, the relationship between the straight trap and his older sister seems to be repaired, thanks to the humorous nature of 'Tentacle Sentry Mode'. However, the constant fighting Seiko is forced to witness Yuki partake in eventually causes the two to have another argument, with Seiko finally berating Yuki for "still embracing the gun." She even goes as far as to threaten Yuki by disowning him if he continues to pursue revenge on Naomi.
This Act ends with Yuki, filled with rage, decking his ghostly onee-chan to the ground with his left hand's fist. He replies to Seiko's threat with his own threat--"Go ahead and disown me~! If you get in my way, I'll make sure to erase you myself." Seiko begins to cry as she becomes torn between her love for Naomi Nakashima and her enraged trappy brother--wanting neither to die.