After Shiki was almost killed by SHIKI Tohno and saved by Akiha Tohno, Makihisa Tohno manipulated Shiki's memories and changed him greatly in order to have him play the part of SHIKI. The remnants of his Nanaya-self were cast away and hidden, only appearing briefly in certain situations. It is not that they are separate personalities, but the same existence. Tohno is an extension of Nanaya even though Tohno forgot him, but while Nanaya is the foundation of Shiki, he is not Tohno's "past."
Nanaya is always calm and composed, and he is prone to making sarcastic and witty comments. He is fixated on death and killing, and the mere prospect of it brings him the utmost joy. He calls his body a guiding principle that Shiki refuses to use in his objections to becoming a killer. He is originally just something that kills whoever summons him, but he later develops an attachment to existing. He mentions having been sleeping when he did not exist, and that there were people to play with on the "other side", though he could not kill them because they were all dead people. Although obsessed with killing, he displays somewhat normal interactions with people like Miyako Arima and Hisui.
Depending on the situation, such as where Nanaya's will intermingles with Shiki Tohno's libidinous desires when seeing Arcueid's Mystic Eye, Nanaya may emerge in the form of venereal madness. Instead of choosing to immediately kill, he raped Arcueid Brunestud while thinking he wants to plunder Arcueid's heart, body, blood, flesh, desires, impatience, sins, and punishment.
Nanaya mostly only emerges in the form of Shiki's killing intent in Tsukihime. He does not have a distinct personality, and it remains mostly suppressed. He fully emerges in Ciel's route after Shiki is close to death after slaying Michael Roa Valdamjong's soul from his own body. He has a realistic dream of a normal, everyday life as he slips closer to death, seeing a small boy peering at him in the hospital and the mansion without saying anything. Upon realizing the nature of the dream, he begins to head towards death as Nanaya speaks to him, telling him to ignore the dream, Ciel's wish rather than his own, and focus on his own needs.
During Kohaku's route, he emerges fully due to the drugs Kohaku had given to Shiki. He walks about outside and encounters SHIKI.
Nanaya first appears in Melty Blood as the direct manifestation of Night of Wallachia in the paths where Shiki being the rumored killer is the most prevalent rumor. He describes himself as Shiki's sin, the end Shiki fears should come if he ever gives into his urges to kill. Wallachia believes Shiki is a natural born killer suited to being a god of death, so it is silly for him to fear becoming a killer if he should ever even slightly err. One path features Akiha being his seeming manifestation, but Shiki's rumors outweigh her own to Wallachia's disappointment. He begins to fade after being defeated, deciding to kill himself in glee because there were no other targets. Shiki's anxiety over Akiha gives him form as her once more before he is successfully repelled.
Another path features Wallachia becoming Shiki instead of Arcueid Brunestud, but he takes joy in the form even though his original plan did not follow through. The pleasure of being able to slaughter with the "god of death's" eyes brings him great satisfaction, and he decides he can wait how ever long it takes to become a True Ancestor. Notably, this is his only incarnation where he possesses the Mystic Eyes of Death Perception. He is defeated, happy with being able to acknowledge what it means to be a "killer." He asks Shiki what it was like to "defeat your sin with your sin", noting that Nanaya is Shiki's sin that could not take shape. Refusing to accept that, Shiki sinned further by penalizing himself with murdering in order to eliminate his sin of murder. He then takes on the form of Nrvnqsr Chaos before being fully defeated.
Nanaya, independent of the influence of Wallachia, is brought forth in Melty Blood Re-ACT by White Len. He notes that it is rude to "wake the dead", having been "starting to enjoy the worst of being dead" to then be trapped in a body of flesh. Without knowing his creator, he comments that raising him is simply asking to be killed. He meets with a manifestation of Akiha's bloodlust, and they both call the meeting fortunate because they can kill each other. He notes that Shiki would be jealous of their brother-sister relationship, where they hide nothing from each other and do not hold back.
He encounters Nrvnqsr Chaos after, and they also are both happy for the meeting. Nanaya considers the previous engagement to not have been a proper fight, and Nrvnqsr believes as he feeds and Nanaya kills, it is only natural for their inclinations to clash. Before they fight, Nanaya exclaims joy in that Nrvnqsr's body can produce more corpses than any other. After the battle, he mentions that having had always wanted to fight him, he has no regrets and that there is only one last task for him. He finally finds White Len, who had been expecting him to simply follow her orders.
She is surprised that he, an illusion manifested by her, would wish to kill her and cause his own death. He does not care about who disappears or remains afterward, telling her that it was her mistaking in waking him. She tries to reason that he is an unused part of Shiki like she is an unused part of Len, but he simply says his purpose is killing and attacks. He encounters White Len's creator, Aoko Aozaki, planning to use his final time before fading away to slay her because it is a dream of his to take her apart. After the fight, he says that the "screenplay" is finished though there was no audience and that the unsuccessful actor will fade into darkness.
Melty Blood Act Cadenza begins the same way as Re-Act, and he has the same meeting with Akiha. He encounters Kishima Kouma instead of Nrvnqsr, and says that they have both been waiting for their meeting. Feeling the most pleasure he has ever felt by encountering Kouma, Nanaya wishes for a "brain-frying fight to the death." With nothing left after the battle, he is surprised to find that he is afraid of death. He, who was nothing, gained something, so he no longer wants to disappear. He realizes it is that he cannot kill anyone after dying because those on the other side are all already dead. Though it is not a pleasing ending, he calls it a fitting punishment and accepts disappearing miserably.
White Len's path ends with her breaking her portion of Len's familiar contract with Arcueid Brunestud after "defeating" her and taking Nanaya as her master. He teases her for running away without checking Arcueid's status, and says that he is overjoyed to have more inconveniences. She bashfully tells him to be more respectful or just disappear, and he simply mentions the effectiveness of their relationship, with him being "good at doing" and her being "good at using." She once again becomes bashful at the implication of having betrayed Arcueid for him, and she simply says that he is the only one she has the least objections with partnering with in the town. Once again mocking her, he says she is scary and that he will be a good master.
Nanaya acts as a familiar to White Len after Act Cadenza, allowing him to continually stay in the world under her TATARI abilities. He also acts as her 'Master' after forming a contract, bringing about a strange relationship where he cannot say which one of them is the familiar. He has mastered the Nanaya Assassination Arts, as opposed to Shiki Tohno who has only learned the basics; however, he lacks the Mystic Eyes of Death Perception in most of his incarnations. One technique is Nanaya's Flash Sheath: Lost Prison Shramana (閃鞘: 迷獄沙門, Sensa: Meigokushamon?), and his Last Arc is Extreme Death: Seven Nights (極死: 七夜, Kyokushi: Nanaya?), throwing his knife straight at his victim's heart and going for an overkill by snapping their neck from above. He is able to kill Shiki Tohno, who has forgotten how to use his Mystic Eyes, multiple times with ease in Kagetsu Tohya.
 Tsukihime Dokuhon PlusPeriod - TSUKIHIME Dictionary: Nanaya Shiki [Person's name], p.186
Shiki Nanaya [Person's name]
Eldest son of the Nanaya, a clan of demon hunters that passed down ESP as their genetic inheritance.
The Nanaya had retired from the demon hunting trade to live a quiet life in the mountains. However, because Tohno Makihisa still regarded them as dangerous, they were raided and completely wiped out.
Shiki, too, was very nearly killed by Makihisa, but somehow he narrowly escaped death and was taken in by the Tohno family as an adopted child.
Though Shiki himself does not remember anything from when he lived in the Nanaya village, he did receive basic training before Makihisa attacked. This training was responsible for turning Shiki into a transcendent killer every time he was backed into a corner during Tsukihime… somehow.
In Melty Blood, Nanaya Shiki appears as Tohno Shiki's anxieties given form. He uses the Nanaya martial arts that Shiki should have learned, but unlike Shiki he does not possess the mystic eyes of death perception. According to Miyako, he is her "wild big brother". Also, perhaps it is due to Wallachia's influence, but he is prone to somewhat theatrical elocution.