If you've been watching boss videos for this game, reading FAQS, or reading extensively about certain demons or characters, then you are probably unable to fathom out the plot. Playing the game is probably no help, due to its insane difficulty. So here's a quick (or, more correctly, as quick as it gets) synopsis of the storyline.
The plot begins with the protagonist (named Naoki Kashima in the novelization and addressed as such for clarity and convenience) taking a train to Yoyogi Park, where he plans to meet with his friends Chiaki and Isamu, so they can go and visit their sick teacher Yuko Takao in hospital. Unfortunately, Naoki is late and Chiaki and Isamu have already left without him. Passingly, he hears a news report about a missing executive from a comms company, Hikawa, and an earlier, brutal riot that ended with fatalities on both sides. He meets a man named Jyoji Hijiri, who gives him a magazine called Ayakashi Monthly, warning him the riot was covered up and that the truth about it had been hidden. Naoki then gets a call from Chiaki, telling him to go to Shinjiku Hygienic Hospital where Ms. Takao is.
Once there, Chiaki scolds him for being late, then, as she's alone in the empty hospital and bored, borrows the magazine as Naoki searches for Ms. Takao and Isamu. He manages to get a glimpse of Isamu through the windows as he returns to the hospital's lobby. There, Chiaki comments the magazine has an article with disturbing information about the Cult Of Gaea, a cult who believe that the world is going to end soon, as foretold in the Scripture of Miroku, their religious text. She then becomes nervous about the hospital (named as the cult's base in the magazine) and Isamu gives Naoki a keycard he found. Using it, he enters the hospital's basement and finds a room with an odd metal pillar connected to machinery, and an annoyed man. The man, Hikawa, proceeds to summon a demon to kill him, but Ms. Takao appears before the demon manages to do so and threatens to abandon Hikawa if he kills her students. Hikawa shrugs and allows them to depart. At the exit, he briefly sees a woman in Western mourning garb with her young charge.
Yuko bids Naoki accompany her to the hospital's roof, where she promises to be his strength and offers some cryptic advice. Then, they witness as a blue starlike object materializes above Tokyo, and with a flash of lightning, commences the destruction of Earth, cutting a section of Tokyo off from reality and enclosing itself on it by collapsing it into a sphere. More black lighting erupts, destroying Tokyo. Humanity dies off in lightning as their city becomes an embryonic world. The Conception has begun.
After this, Naoki drifts between dreams and reality, where a shining white light scans his soul. Finding no definite drives or ideals, the being casts him away to discover himself. He then drifts into another state, where the boy and his nanny from earlier materialize before him. The boy, obviously amused by him, whispers to his nanny to hold him down, as he drops a wriggling bug into Naoki's eye, which claws its way into his head as the woman mutters the entity, which she calls a Magatama, will make him a demon.
Waking up in the hospital's morgue, he finds his body warped, with shining tattoos covering his anatomy and a horn growing on the back of his head. Leaving the room and back into Hikawa's room, he finds Hijiri again. Hijiri promises to study what has happened while Naoki, now a half-demon, leaves to explore with the powers he's been granted. As he leaves, he is spirited away to a tunnel of rusting walls, with a flowing red liquid filling the walls and floor, and meets an old man in a wheelchair and a young woman in black, who test Naoki's new powers by setting some demons against him. Finding him to be adequate, they communicate to him through a sort of station and sending him back to the hospital.
Searching the hospital, Naoki cannot find Chiaki and Isamu, but discovers a demon known as Pixie. She's trying to get to the Annex, which is currently the only way to leave the building. She informs Naoki that the ID Card for the Annex is being held by some Pretas, who have barricaded themselves inside a hospital room. The two join forces to try and get out of the medical centre.
Outside the Pretas' room, Pixie imitates one of them, telling the ones inside that she has a lot of Magatsuhi, something the Pretas want. The duo enter the room and defeat the Pretas, taking their Key Card. Naoki discovers that he can talk to demons to convince him to join him. Naoki's new army heads into the Annex and defeats the demon Forneus, who, furious at missing a human as he left the building, tried to kill them. Outside the Medical Centre, the party discovers that Tokyo is now a giant hollow world known as the Vortex World with the pale blue star as its center. They explore, and meet several Souls, who are the ghosts of some of those who died in the Conception (everyone outside of Shinjuku Hygienic Hospital) The Little Boy appears and informs Naoki that the star is called Kagutsuchi, the Divine Light, as a demon hunter named Dante passes nearby.
Naoki and Pixie go to Yoyogi Park per her wishes, since the fairies have made their base inside. There, she says goodbye to Naoki, but Naoki begs her to stay on, so she decides to stay. Naoki and his group go to Shibuya, where they discover Chiaki. She is not shocked by Naoki's new appearance, but is surprised that what was detailed in Ayakashi Monthly came true. She departs, and Naoki gets some information from a Nekomata that he should go to Ginza to find Isamu and Ms. Takao, as they have probably been captured by the Assembly of Nihilo, one of the organizations born in the wake of Old Tokyo to seize control of the Vortex World.
Exploring Shibuya, he finds Hijiri again, inside a Terminal, a room that contains an Amala Drum, as the pillar's called. Hijiri has figured out how to use the Amala Drums to enter the Amala Network that connects them, and offers to let Naoki in and guide him to Ginza. However, the two lose contact with each other, and Naoki ends up fighting a creature named Spectre to get out. As he leaves, he is again transported to the communications chamber used by the lady in black and her elderly boss. The Lady in Black explains that she and the Old Man lost the set of Candelabra at the hands of terrible Fiends, and asks Naoki to recover them all. She also allows him to go to the Labyrinth of Amala, which requires Candelabra to enter. It is a dangerous area, full of deadlier demons, but also holding rare treasures and contains secrets about the Vortex World's purpose. As first part of his mission, they give him the Candelabrum of Sovereignity, telling him it will attract the others and their bearers. In Ginza, he heads out to the Assembly's Shiodome base, only to be kicked out by a large demon, Berith. Searching in Ginza, he receives information from local bartender Nyx that he should go to Gozu-Tennoh, leader of the Mantra Army, Nihilo's enemies.
In order to get there, Naoki goes into Harumi Warehouse, and down into the Great Underpass Of Ginza. Inside, he meets people named Manikins, who twitch violently for some reason and are deathly scared of the Mantra Army. Naoki is stopped from going to Ikebukuro, home of the Mantra, by a Manikin guard, for security reasons, so he goes to the Collector Manikin, who is allowed to leave the Underpass, for help. The Collector asks him for a 1000-Yen Bill, and Naoki uses the Amala Drum in the Underpass to return to Ginza.
In Ginza, he finds local drunkard Loki has a 1000-Yen bill, but intends to charge him an astronomical sum in exchange for it. Naoki does find, however, a back door to Loki's room, and is forced to kill the Troll guard to get in and steal the bill. The Collector Manikin then gives him a letter of passage to reach Zoshigaya Cemetery. On his way out, however, the Candelabrum of Sovereignity starts flickering wildly and ends up getting him sucked into another dimension for a battle against the Fiend Matador, who drops the Candelabrum of Foundation, which opens the First Kalpa of the Labyrinth.
In Ikebukuro, he enters Mantra Headquarters, only to find Isamu assaulted by the Mantra's second-in-command, Thor, for the crime of suspicion of being a Nihilo spy. Thor violently draws out a red substance from Isamu and empowers himself with it before ordering Mantra guards against Naoki. Transported to the Mantra's Court, Naoki is forced to win a trial-by-combat, earning his freedom. He is escorted out to allow him to recover. However, at the east Ikebukuro, Naoki finds another of the Candelabra's "thieves", the funeral demon Daisoujou, and wrests the Candelabrum of Eternity from him. Upon returning to the Mantra, he is ambushed by and battles Dante, who leaves on his own without further discussion after a brief, one-sided scuffle in Dante's favor. Before leaving, though, Dante comments he'd been hired to retrieve the Candelabra as well by the Old Man.
Within the Mantra's top floors, Naoki meets the army's leader: the powerful demon Gozu-Tennoh. Gozu-Tennoh is interested in Naoki's power and increases it by allowing him more demonic contracts. He then asks the teenager whether he'd like to join the Mantra. Regardless of the answer, Naoki then unwittingly prompts an attack from the Mantra upon the Assembly's Shiodome. Leaving for Ginza, he arrives at the Shiodome to find it cleared of Nihilo demons and the core unit of the machine they'd been using to siphon a free-floating red substance broken. However, he finds Hijiri at the Core Unit, and he's told that the Mantra have been fooled into attacking a dummy base. Sure enough, even further investigation reveals Nihilo's true base is further below. Naoki is forced to keep pressing the attack in hopes of shutting the machine down.
At the True Core, he finds Hikawa, who, while astonished at the fact he was still alive, had no need for him, commenting he knew where Yuko was. Idly musing about Magatsuhi, the red substance being drained by the Shiodome and which Thor had taken from Isamu, Hikawa clarifies it's actually a form of energy generated by human psyches and can be used as offerings to gods and demons as a channel and power source. He then talks about something he called a Reason: a philosophy or way of life that could be used with Kagutsuchi's power to recreate the world according to its laws. He then summons Ose, who confronts Naoki to remove him from Hikawa's concerns as Hikawa himself activates something called the Nightmare System, which uses Yuko herself as a component, and teleports away. After the battle, as he lays dying, Ose tells Naoki that the Nihilo will win anyway.
Back in the Mantra's HQ, all are suddenly weakened, and Naoki discovers that the Nihilo are draining them of energy using the Nightmare System, a focused version of their old Magatsuhi-siphoning device. He runs into Chiaki again, and discovers that she is going to create a Reason, a path to a new world to replace the old one. She decides to call her Reason Yosuga, a world where the strong kill the weak and reign supreme. Upon reaching the top floors, he finds Gozu-Tennoh's body crumbling under the relentless siphoning, with the deity angrily promising never to allow Hikawa and Nihilo to impose their brand of empty power into the new world to come. Thor releases Isamu and the other prisoners; Isamu decides to find Ms. Takao and asks Naoki to help as well.
They decide to go to Kabukicho Prison to find a future-reading Manikin who can help with their search for Yuko, with Naoki battling Hell Biker on the highway between Kabukicho and Ikebukuro, and winning the Candelabrum of Dignity. Naoki discovers that Kabukicho Prison is essentially a Manikin torture chamber, with the Mizuchi jailer and the Naga guards often abusing their prisoners for more Magatsuhi. With help from the Collector Manikin, he defeats Mizuchi, and saves Futomimi, the leader of the Manikins. Isamu renounces his faith in Yuko and Naoki due to being captured earlier and tortured for the second time, and, with an Amala Drum he was imprisoned next to, plans to form the Reason of Musubi, where everyone rules their own part of the world and cannot interfere with anyone else, with the knowledge of the Amala Network.
Futomimi reads Naoki's future to thank him, and tells him of a man in Ginza. When Naoki returns there, he finds that the man is Hijiri. They plan to stop Nihilo using the Terminals, but the one he is currently looking at is under their control. He tells Naoki a rumour of one in Asakusa, a town that the Manikins are rebuilding, so Naoki heads to the East Ikebukuro Station to find the Ikebukuro Tunnel. All the Souls there tell him of a large group of Manikins who went into the Tunnel.
In the Tunnel, the Manikins and Souls are raving about a group of four strong oni, and Naoki realises that they are referring to Fuu-Ki, Sui-Ki, Kin-Ki, and Ongyo-Ki, who Thor expelled from the Mantra a while ago. He defeats the first three, and Ongyo-Ki tries to trick him by creating doppelgangers of himself, but Naoki fights him during a Full Kagutsuchi, the light entering the tunnel and negating the oni's illusions. Naoki reaches Kuramae Station, and then Asakusa, which turns out to be an ex-slave town for the Manikins freed from Mantra oppression. Hijiri manages to join Naoki in Asakusa using the Terminals.
Hijiri tells him that the Manikins are created from the black mud from a river that flows near Asakusa, explaining why they wanted to rebuild it. Naoki is advised by Hijiri to look around while Hijiri finishes his investigation into the Nightmare System. Some of the Souls are upset that the Manikins have taken over, while others think that it is heartwarming seeing them restoring Asakusa, but ultimately saddening when one looks at the bigger picture of Nihilo's growing control over Tokyo. Inside the Labyrinth of Amala, after completing the First Kalpa, at the end of the gilded marble tunnels, the Lady in Black talked to him again, revealing him part of the truth about the Conception. Kagutsuchi is a fragment of the Great Will's power. Every universe has a finite amount of energy, and when it has been expended, it can either undergo the Conception or die. The force responsible for the death and rebirth of countless universes, each with Kagutsuchi as its core, is the Great Will. The Lady in Black's master has long pondered the purpose of the cycle of death and rebirth, and she reminded Naoki his power had been a gift, not to be squandered.
As Naoki enters the Second Kalpa, he discovers a mighty voice warning him at the entrance to leave and never return. A nearby demon identifies it as the voice of the Great Will, unnerved it was able to sense what transpired even in the depths of the Labyrinth. Scattered across the Kalpa are the souls of several people; some from a religious order named the Order of Messiah, and some from a rival cult known as the Cult of Gaea. The Messians believe in a world of law and obedience to their single God, while the Gaians want to live in harmony with the gods of the Earth. The Messians snarl about the Gaians' impiety and their lawlessness, while the Gaians rant about the Messians' brainwashing and mindless submission. Both parties had intended to stop the Conception, but had been wiped out by Hikawa in the Yoyogi Park riots to fuel the advent of the Conception. At the end of the Kalpa, the Lady in Black communicates again to provide annotations, this time, on Hikawa.
Hikawa had once been a member of Gaea; even though the cult had an all-inclusive policy, seeking to meld allreligions, ideals and beliefs, even diametrically-opposed ones, his had been an extremist view that had branded him a heretic. He had, however, found the full Scripture and the requirements and rules of the Conception. He had orchestrated he riots to kill off his rivals and trigger the rebirth of the world, and was ever closer to finding what he needed. Reminding Naoki that an alternative was forming and that he could prove pivotal in triggering it, the Lady in Black faded. As Naoki entered the Third Kalpa, he was greeted with the four knights of death: the Four Horsemen of the Apocalypse themselves. Each held one of the Candelabra needed to further continue, and warned/promised to wait in the Vortex World to be challenged; they had been silent witnesses of the gears of Fate for aeons, and confirmed an exit had been prepared, though it could have a high cost for Naoki himself and his humanity.
Naoki returns to Kabukicho Prison, where he discovers that Hee-ho, a traveller who wanted to become as strong as the great emperor, King Frost, is now ruling it and has frozen everything and populated it with Jack Frosts. Naoki defeats him and returns to Asakusa, making a detour at Shibuya to stop some Manikins who are forcing a Baphomet to summon Mara for revenge against the Mantra. Mara manifests, but is in an incomplete and slimy form, so Naoki easily kills and banishes the god of temptations.
In Asakusa, Naoki beats the White Rider, and in the Underpass, the Red Rider, getting the Candelabra of Compassion and Insight respectively. Back in Asakusa, the Manikins have been attacked by Sakahagi, a murderous traitor. Naoki and his demons go and finds Sakahagi, driving him out of Asakusa, then return to Futomimi, who's been meditating alone at Mifunashiro, the core of Asakusa and the Manikins' holy site. There, he announces he will devise a Reason of Manikins, allowing everyone to live in peace and happiness. Naoki returns to Hijiri, who has finished his investigation. Hijiri shows Naoki a picture of the Obelisk, a monument that Nihilo is using as the home of the Nightmare System. Using the Amala Network to return to Ginza, Naoki goes over the Rainbow Bridge to Nihilo's new base.
Inside the Obelisk, he defeats the Moirae Sisters Clotho, Lachesis, and Atropos, by themselves, and then all of them together. At the Obelisk's top level, Yuko was being held as the Nightmare System's main pillar; upon removing her from the structure, the System was shut down. Yuko awoke slowly, berating herself for depending on her student when she had promised to be his strength. Yuko identifies a goddess known as Aradia as her Demonic Sponsor, the god backing her request for a new world. Aradia appears by possessing Yuko's body; she Aradia increases Naoki's power and leaves, annoying the Old Woman in Black and the Little Boy. The Old Woman in Black says that the Little Boy delights in Naoki's suffering, and that Naoki must entertain him. The way he can do so is to make the world into a war based around the Reasons, as the "time of Creation" for the Vortex World is near.
Back in Asakusa, Hijiri says that one of the Reasons is going to be the basis for the next world. In order to make it so, however, a Reason Holder must summon a Demonic Sponsor with large amounts of Magatsuhi, explaining the Nightmare System's purpose. In addition, Hijiri heard Isamu in the Amala Network. With the help of a female soul named Kamala in the First Kalpa, Naoki finds the Black Rider in Shinjiku Hygienic Hospital. He gets the Candelabrum of Wisdom from him, then goes to find Isamu with Hijiri's help, until the connection breaks down again. Naoki runs into Spectre again, who tries to get revenge but fails, dying for good after his final aggression.
All the Souls in the Amala Network (and some of the demons) preaching their belief in Musubi. Inside an Anomaly, Isamu officialy creates his own Reason by fusing with some of the spirits of Amala, before vanishing to make Naoki feel alone, so that he can understand Musubi. In the Third Kalpa, Naoki meets up with Black Frost again; realizing he still wanted to get stronger, and reasoning that joining the one who defeated him earlier is a good way to start, Frost joins him, getting the first taste of battle with his new master as they are chased by Dante again. Dante then reveals that he was hired by the Old Man to find the Naoki, and now the Old Man wants to see them battle. Afterwards, Naoki is cornered by him, and they fight. Barely managing to withstand Dante's attacks enough to convince him to drop it again, the Demi-Fiend successfully survives. Dante decides to give Naoki his Candelabrum of Knowledge, and decides to look for the Old Man, freeing Naoki from his pursuit and allowing him to reach the end of the Kalpa, where the Lady in Black and her master await.
The Lady in Black comments Aradia comes from a dying universe, has invaded this one to try and become a Demonic Sponsor, and has tricked Yuko into serving her with the excuse of giving her a Reason. After returning to the Vortex World and investigating a rumour that there was a human in Ikebukuro, he decides to go and check out a prophecy Futomimi divined in Mifunashiro, the Manikin's holy land, during a period of meditation. In the new area of Asakusa, Naoki defeats the Pale Rider, getting the Candelabrum of Majesty. He then follows rumours to Yushima Station, which is full of slaughtered Manikins, and goes to Gaien-Mae Station via the Asakusa Tunnel.
In Yoyogi Park, the demons and Souls are talking about disasters and a crazed Manikin. Naoki finds Yuko again, and the two discuss her Reason; Yuko comments she is sure Aradia will give her a Reason if she gives her a special stone, the Yahirono Himorogi, which is full of Magatsuhi. However, the stone is in the grasp of Sakahagi, and she offers the Magatsuhi to Naoki in exchange for the stone. Naoki then leaves into the Construction Site and is attacked by waves of Pixies and High Pixies. Naoki then finds Sakahagi; the demented Manikin, wishing to stand tall above man and demon, wastes the stone's Magatsuhi reservoir to summon a powerful demon, Girimekhala. Naoki, however, is able to prevail over the crazed pair with his demons and killed them both. It turns out that the fairies had been reduced to their primitive nature by a curse from Sakahagi. Oberon, king of the fairies, mentions that a girl had earlier confronted Sakahagi and been badly hurt. Naoki gives the stone to Yuko, in the hope that she will be able to use it to get a Reason out of Aradia (Yuko is unaware/unable to understand that she must establish a reason herself).
Passing by Ikebukuro, Naoki met Hikawa again. According to him, Naoki is the Demi-Fiend, the one who must shape the new world from a Reason, but he cannot create his own, due to the Magatama making him half-demon. Hikawa is aware he must have the Demi-Fiend's backing to create his world of silence, as written in the Scripture of Miroku, so he expounds on his Reason; Nihilo espouses a philosphy of nothingness, decrying individuality as the source of all of Humanity's problems and believing in all beings as mere cogs in the great machine of the universe. Considering his answer, he informed Naoki that he was wary of the resurgence of the spirit of Gozu-Tennoh.
Naoki defeats The Harlot for the Candelabrum of Beauty, and she expresses total confusion at his act of giving away the Yahirono Himorogi after such a hard battle for it. Naoki continues his investigation at Ikebukuro, and discovers that Gozu-Tennoh has infused Chiaki with the remanants of his power after her brutal defeat at Sakahagi's hands. Chiaki receives great power and mutates as Isamu did, restoring her arm into a mass of tentacles and warping her body, thus establishing Yosuga. The demons of the Mantra and the Divine lineage hail Chiaki as their new leader.
In Asakusa, Hijiri now has access to the knowledge of Amala, and knows everything. Hikawa is in the Diet Building, getting Magatsuhi, while there is a temple filled with it elsewhere. Meanwhile, Manikins in Mifunashiro are demanding their own Reason. Hijiri refuses to tell Naoki anymore, realizing that he could create his own Reason, and prepares to kill the Demi-Fiend for his Reason. However, Isamu captures him and tells Naoki that to save him, he will have to defeat the three demons guarding a large store of Magatsuhi at the Amala Temple. He defeats Aciel in the Black Temple, Albion in the White Temple, and Skadi in the Red Temple. The Magatsuhi flows, and Isamu fulfills his promise, letting him into the central temple so that he can tell him the truth of this world, and of Musubi.
Isamu is the one who carries out Hijiri's execution, using his Magatsuhi to summon his Demonic Sponsor. Angels arrive and, witnessing the birth of Musubi, go to find their leader Chiaki, who is in Asakusa. Fearing for the Manikins, Naoki returns there, and goes to Mifunashiro, where Chiaki has massacred the Manikins for their Magatsuhi. Chiaki makes Naoki waste time fighting the three Seraphs Uriel, Raphael, and Gabriel, so that she can kill Futomimi. Chiaki steals his supply of Magatsuhi (which he was gathering create a Reason, unaware that Manikins could not do so) and summons Baal Avatar, her Demonic Sponsor. Naoki returns to Asakusa, which has become a slum filled with Mantra demons. Naoki goes back to Ginza after hearing rumours about it, and Nyx, who told him about the Mantra, tells him that Nihilo is moving into the Diet Building for Magatsuhi. Naoki goes to Yurakucho Station, and defeats the last fiend, Trumpeter, receiving the Candelabrum of Godliness.
Deeper into the Fourth Kalpa, Naoki encounters a bizarre tunnel known as the Twelve Meters of Eternity, which shifts its destination according to the phase of Kagutsuchi. One tunnel leads him into the Road to Hell, a simple path that leds him back. Another leads into Hell's Treasury, a zone of vaults bursting with coin but riddled with teleporters. Yet another path leads to Hell's Maze, an are where lost souls are forced to wander for eternity. There, in two chambers, he finds two coloured Souls - a business man who lost all his money, and a teenage murderer. Hearing a rumour about an Afterlife Bell, Naoki goes back to Zoshigaya Cemetery, and finds it in the hand of a stain shaped like a human; further investigation will reveal it was a Manikin who used it to become human, not knowing doing so would doom him instantly. Allowing the two Souls to hear the Bell's ringing, they leave Hell's Maze for a chamber where all souls wait to be reborn, and they turn out to be Futomimi and Sakahagi, with Futomimi being the murderer and Sakahagi the once-respected businessman.
In the darkest section of the Fourth Kalpa's Twelve Meters of Eternity, Hell's Hall, Naoki fights Beelzebub, second-in-command to Lucifer The immense Lord of the Flies lightly chides the young Demi-Fiend for so blindly following the path offered by his master without having any idea of what it exactly entailed, but offered the fact the candelabra are used in conjunction to create a new demon of Chaos as compensation. He also offers his help to Naoki, provided he can prove his worth to the cause of Chaos. Following a grueling battle against Beelzebub, the Curse Zones are lifted, and Naoki is now able to pass through them safely. At the communication station at the end of the Kalpa is revealed/implied by the Lady in Black that Hijiri is Aleph from Shin Megami Tensei II
, who is being punished for deicide by being forced to be reborn in a new world during each Conception, and being powerless to stop it, only able to record it. To stop him from being able to change anything, he always dies.
Naoki realizes after a few tries that a special key is needed to progress, and an Efreet comments that his drinking buddy has it. Remembering frequently seeing Loki drinking, he goes to Ginza, to find that Loki sold it for liquor, as his room was raided by a certain someone earlier in the game. Naoki goes to see the Collector Manikin is his store and gets it from him.
Back in the Fifth Kalpa, Naoki uses his own Candelabrum of Sovereignity to open the Kalpa's door, and meets Dante inside, recruiting him. A special door in the depths of the Fifth Kalpa can only be opened by the original Pixie recruited in the Hygienic Hospital, and it empowers Pixie to the ultimate degree, augmenting her power so she's a virtual powerhouse befitting her master. The loud voice that told Naoki to turn back in the entrance of the Second Kalpa reveals itself as Metatron, who Naoki manages to take down. Back at Yurakucho Station, Naoki makes his way through the Yurakucho Tunnel to Kasumigaseki Station, and enters the Diet Building. He defeats Surt, Mada, Mot and Mithra, then enters the top room.
Yuko meets with Hikawa as he summons his god and establishes Shijima, as Naoki fights Samael, Hikawa's second-in-command. Aradia manifests and talks to Hikawa, trying to convince him not to force the cration of the world of Shijima to favor a world of freedom, pointing out his belief in Shijima was in an on itself a kind of freedom. Decrying Aradia as a foolish voice who could not even protect her single follower and Yuko as a coward who could never get her own Reason due to her fears and timidity, Hikawa summons Ahriman, god of the void. Aradia escapes to the world about to be born, abandoning Yuko at her request. Yuko, believing both worlds would die if left to Hikawa's devices, dies as Ahriman fully manifests. As she dies, she gives Naoki the Yahirono Himorogi, in the hopes that he can create a world from it.
Naoki, for the last stretch of the journey, returns to the Amala Temple and sets the Yahirono Himorogi at the central temple, sending a beam of Magatsuhi at Kagutsuchi, making him extend several long, stony appendages, one of which slams into the Obelisk and rams it into the ground, transforming it into the Tower of Kagutsuchi. As he enters the enormous structure, Kagutsuchi again scans his heart to determine his Reason (locking his alignment) and bids the Demi-Fiend reach him at the final floor of the Tower.
From here onwards, the ending changes depending on the alignment choices taken throughout the game.
- True Demon Ending: Naoki finishes the Fifth Kalpa before entering the Tower and discovers from the Lady in Black that they did not lose the Candelabrum at all - they gave them to the Fiends, and Naoki is one of them, explaining why he received the Candelabrum of Sovereignity. He discovers that God is restarting the world through the Conception with his avatar Kagutsuchi over and over again until all free will is gone and he rules supreme. Naoki is selected as the one who will bring down God, as the master of all deaths. By acknowledging the desire of his new master, he is stripped of the remnants of his humanity, converted into a full demon, sent back to Shinjiku Hygienic Hospital's morgue, and told that he must take down the Reason Holders.
- He goes to the Tower of Kagutsuchi, and defeats Ahriman (the union of Hikawa and his god), Noah (Isamu's god) and Baal Avatar (Chiaki being empowered by her god). He then proceeds to kill Kagutsuchi and, showing him a Reason of absolute destruction, which would shatter the plan set out by the Great Will, thrusts the multiverse into darkness. The Old Man then shows up, and tells Naoki that he is the same being as the Little Boy. He then reveals his true form - as Lucifer, and when Naoki wins, takes him to the last battle, against God. The game ends here, and the player does not get to see the battle between Naoki and God.
- The only requirement is to reach the lowest layer of the Fifth Kalpa before entering the Tower of Kagutsuchi.
- Demon Ending: Naoki reaches the Tower of Kagutsuchi and confronts all Conception gods, eventually reaching Kagutsuchi. However, he has demonstrated his weakness of character by admitting he still fears ridicule and still carries a strong fear of failure to Aradia; therefore, Kagutsuchi fades unfought, leaving the Vortex World unchanged.
- Lucifer praises the Demi-Fiend for the creation of a realm of only demons, but warns it will remain as such until the next Conception.
- This ending is achieved by following more than one Reason or rejecting all three Reasons and admitting fear of ridicule and failure to Aradia, revealing himself as a coward unable to sustain his own resolutions.
- Shijima Ending: At the Tower of Kagutsuchi, the Demi-Fiend will meet with Ahriman and will be granted passage. The battles against Noah and Baal Avatar procceed unchanged.
- After being defeated, Kagutsuchi unleashes his power willingly to create the world of Shijima. The Demi-Fiend is thanked by Hikawa for allowing his vision to come true, hailed as the true champion of Shijima.
- This ending is achieved by following Hikawa's resolutions and always agreeing with him.
- Musubi Ending: The battle against Noah is skipped, as it's revealed he was slain earlier against Baal Avatar. Kagutsuchi also unleashes its power willingly to create Musubi's World.
- After the defeat of Kagutsuchi, the Demi-Fiend finds a stone slab with an inscription by Isamu, who thanks him for his help and wishes him well in the new world to come.
- This ending is achieved by following Isamu's resolutions and always agreeing with him.
- Yosuga Ending: All Conception gods are fought, as Yosuga by definition requires its strongest to face Kagutsuchi, and the title can only be awarded in death matches. Thus Baal Avatar also dies at the Demi-Fiend's hands, but this time, she expresses glee as her supreme warrior is born.
- Kagutsuchi also releases its powers to create the world of Yosuga. After Kagutsuchi's defeat, the Demi-Fiend is visited by Chiaki's ghost, who earnestly praises him for his prowess and asks him to say hello to the new world on her behalf.
- This ending is achieved by following Chiaki's resolutions and always agreeing with her, as well as Gozu-Tennoh's.
- Freedom Ending: All Conception gods are fought, as well as Kagutsuchi. The divine being is insulted that after all the trials and perils of the Vortex World, the Demi-Fiend has still chosen to restore the world, drunk on freedom as was the Lightbringer before him. Infuriate, Kagutsuchi refuses to recreate the past world and tries to kill the Demi-Fiend, but as it shatters, it becomes obvious it does not have a choice in the matter: the world unfairly killed before its time will be reborn.
- Naoki, apparently restored to human shape, wakes back in his apartment, where he is visited by Isamu, who has been reborn without memory of the Conception. Together, they join Chiaki in their visit to Yuko, whose faith in Humanity has been rekindled and hopes to make a full recovery, thanking the warrior who kept the light when she could not.
- A final e-mail from Lucifer reveals Naoki has actually kept all of the power and memories he accrued during the Conception, for the Great Will's pattern has been disrupted and he will need them one day, when he's forced to take the blade again and defend his world...
- This ending is achieved by following more than one Reason or rejecting all three Reasons and admitting to Aradia he no longer fears anything, having transcended fear in his quest to restore the world.
The Demi-Fiend can dismiss Pixie, not enter the Labyrinth Of Amala, skip most of the Fiend battles; only Matador is mandatory (and the entire Labyrinth can be ignored by denying the chance), Daisoujou is optional, Hell Biker is mandatory but only appears if you beat Daisoujou, the Riders only appear after breaching the Third Kalpa, and Dante is only recruitable if you entered the Fifth Kalpa, The Harlot is optional, and Trumpeter only appears if the rest of the Candelabrum Trial has been completed.
If following Yosuga, there is a possibility the Demi-Fiend will fight Futomimi instead of the three Archangels.
If following Shijima, Ahriman will grant the optional membership of his servant, Samael. The battle at the Diet Building against Samael will not take place.
In any path, if all 24 magatama are collected, the Demi-Fiend can receive the Lord's Blade from the Master of the Cathedral of Shadows, granting him access to the Bandou Shrine extra dungeon and the possibility to get the 25th magatama.
If you are thinking "I'm playing an old Japanese copy. There's no Fiends, no Amala Network, no Labyrinth of Amala, no Lucifer, and no True Demon Ending! Did I buy a bootleg?" then the answer is no, you didn't. The version that got translated was the Updated Re-release
, Nocturne Maniax
, which added all of the features listed above. The original version only includes about 10% of Maniax