- Before the main events of the game, Clear served under Toue (his original master) along with his brothers α and α2. They were all designed to sing "Dye Music", a song that could brainwash people into submission, literally dyeing their brains, hence the name. The real name he went by was not a name at all, but a serial number, R-2E-054. He ended up defective and was supposed to be disposed of, but the man in charge of the disposal instead took Clear away. The man (later revealed to be the one Clear called his "grandfather") modified Clear, removed his serial number and kept him a secret from Toue and his associates until his death. He treated Clear like his own son; Toue comments that he must have been a single, lonely man to go through all the trouble of hiding him. After his grandfather's death, Clear began living on his own, often taking long walks around the Old Resident District.
- After Aoba's drive-by with Noiz, Clear hears Aoba's voices and tracks him down all the way to Heibon. He was most likely walking along rooftops as he first appears to fall from the sky, startling Aoba. Unsure whether he was dead or alive, Aoba tries to prod him, and is surprised when Clear gets up as if nothing happened. After an odd encounter and officially proclaiming Aoba as his "master", Clear pulls out an umbrella from his coat pocket and walks off.
- Later in the game, Aoba gets out of bed and goes out to the balcony for some fresh air when he hears a faint song outside. As he opens the door to the veranda and peeks out, Clear comes down and surprises Aoba. Clear says that he was on the roof and that he was singing a song called the "Jellyfish Song". Clear talks a little about jellyfishes, confusing Aoba who listens intently despite his confusion. Clear explains his grandfather was the one who taught him the song. Clear then takes out his umbrella and Aoba asks why he carries it around. He replies that he always thought the stars in the sky looked like they were about to fall. Aoba can see nothing but buildings blocking the view when he looks up to the sky for said stars. Remembering something, Aoba then tells Clear that he would like him to call by his name instead of "Master", but Clear insists otherwise. He then goes on to exclaim how cool Aoba was when he wanted to rescue Mizuki (hearing Aoba's other self) but saying that now, even though he's different from before, he still finds Aoba to be really cool. Not completely understanding what he is saying, Clear tells Aoba that he'll protect him and that he'll follow him wherever he leads him. Clear closes his umbrella, gives a polite bow, and motions Aoba to go to bed explaining that he's going to stay up to sing a bit more. They exchange parting words and Aoba goes back to his room. Aoba's bad mood turns into a relaxed one and he falls asleep listening to Clear singing.
- Virus calls Aoba telling him that his house is surrounded by the police, asAkushima claims Aoba is a terrorist. Tae tells Aoba to escape the house with Koujaku, Mink, Noiz and Clear through the back door. While running, Aoba hears Clear calling for him from behind. The two then run together, until they lose Akushima and the police. Aoba is then sent the next installation of Silent Oath, and receives an invitation to Platinum Jail. The two then enter Aqua Forest; a translucent, magic-like place with lots of greenery.Upon checking the invitation again, they notice a location marked on the map, indicating a place for them to stay. They head to Glitter and look around the place. Whilst Aoba is exploring the bottom floor, Clear calls up from the stairs, informing him of the upstairs bedrooms. He also mentions that he'd like to discuss something, before promptly changing the subject to how long the day has been and that it would be a good idea to rest.
- Whilst Clear is sprawled out on his bed, sleeping with his gas mask still on, Aoba decides to check out what sort of channels are available on TV. He decides to stick with the news, and watches an interview with Toue, in which Toue discusses his ideals, and explains he wants to make the world a place free of hardships. Finding it repulsive, Aoba turns off the TV, holds Ren close and falls asleep on the couch.
- Despite falling asleep on the couch, Aoba wakes up on a bed in a sparkly clean room, to the smell of delicious food. He follows the smell to the kitchen, where he finds Clear, wearing a part for his gloves, gas mask and an apron. Aoba kicks him, finding the situation ridiculous. Clear tearfully tries to explain that he heard wearing nothing but an apron was a man's ultimate fantasy, thus he assumed Aoba would like it as well and wanted to make him happy. Hearing this, Aoba feels a little guilty, and decides to try some of the food Clear made for him. He comments that the food is good, and the morning's events end on a good note.
- The two then decide to head out and try and gather some information as to how to infiltrate Oval Tower. Clear explains that he has an idea as to who would know how to get into the Tower, before calling out a police officer. Aoba pulls his mask back tight to muffle out the sounds of his yelling, then pulls him aside to ask just what on earth he was doing. Clear explains that he was always taught that when something comes up, you can ask a police officer and Aoba has to explain that as they're from the Old Resident District, they could be arrested for being 'terrorists'. Clear then begins to walk off, having from someone else that he supposes will be able to help them, much to Aoba's annoyance.
- This time, the person that Clear has deemed to be helpful is visibly sketchy, covered in scars. Clear begins conversing with the hoodlums in a polite manner, as they threaten him and ask for his money. One of the hoodlums attacks Clear, and he blocks, insisting that he mustn't resort to violence. The leader turns up, and pushes Aoba to the ground, which sets Clear off. He proceeds to beat up the gang members, and insists that the leader apologize to Aoba. Aoba manages to calm him down, and the two return to Glitter.
- Upon arriving back at Glitter, Aoba scorns Clear for his earlier behavior. Clear takes the scolding half put-out like a child, then suddenly interjects by enthusiastically announcing that it's now night time. Aoba explains that it's always night in Platinum Jail, leading Clear to clarify that it's now night time, and that he should be getting to bed. He falls onto the couch and falls asleep seemingly immediately, again, to Aoba's annoyance. Aoba reaches for his gas mask, curious as to what sort of expression he's hiding at that moment, and is suddenly grabbed. Clear asks if Aoba would like to see what's under his mask, and Aoba explains that he doesn't mind if Clear doesn't wish to show him. Clear, however, explains that he would happily show Aoba his face.
The next morning, Aoba awakens to find Clear missing. He receives a phone call from Clear, who explains he's successfully infiltrated the tower, and sends him a childishly drawn map, similar to the map he drew when the group was trying to find Tae. Reluctantly, Aoba puts Ren in his bag and heads off to find Clear, following the map he's been sent.
It doesn't take long for Aoba to realise that the place Clear's map has led him to is nowhere near Oval Tower, and he soon finds himself standing in front of 'Overr Tower' (please note, in Japanese 'Oval Tower' and 'Overr Tower' would be pronounced the same), where he receives a call from Clear. Aoba tells Clear that he thinks he was sent the wrong map, and Clear disagrees, telling Aoba 'I'm right up here.' Aoba looks up to see Clear at a window, waving down to Aoba.
Aoba looks back down, notices the sign reading 'Overr Tower' and sighs. He then turns back to his coil and tells Clear to get down from there, and explains that he's made a mistake. Clear, feeling incredibly guilty, comes down from the tower hanging his head and apologises profusely. Aoba sighs again, and suggests they just go home now.
Along the way home, Aoba takes a detour and scolds Clear, telling him to be more careful in the future, to which Clear apologises to yet again. As Aoba turns to continue walking, Clear stops in his tracks. Aoba turns around and asks what's wrong, to which Clear leaps forward and grabs Aoba's arm, breaking into a sprint.
Confused, Aoba asks what's wrong again, to which Clear simply says they have to run. Aoba asks why, and Clear explains they're being chased. Aoba turns his head and sees nowhere there, and, being sick of Clear's idiocy, shakes him off and tells him firmly that he could simply be imagining it. Clear disagrees, and begs Aoba to believe him and to just run with him. Aoba gives in and runs on ahead with Clear.
After running for a while, Clear stops and announces that it's no use, and that they're surrounded. Moments later, Aoba hears people approaching from both directions. The people that appear are the same hoodlums Clear previously beat up, and they want revenge. Aoba retaliates, but is soon held down by the gang members. Clear begs them to let him go, and the head bargains that if Clear is obedient, they'll let Aoba go.
Clear gives in and is held with his hands back. The leader reaches to take Clear's mask off, and Clear knees him in the stomach. The leader pulls Clear's head down to the ground in retaliation, and kicks him repeatedly, and the other gang members follow suit. Aoba yells for them to stop, and regrets not believing Clear in the first place, thinking that maybe if he'd run immediately, they wouldn't be in this position. The leader of the gang then pulls out a bottle of sulfuric acid, and pours it on Clear's head, laughing.
Aoba cries out Clear's name, his legs trembling, to which Clear calmly replies and stands up. He asks if the thugs are done yet, and then asks them to release Aoba. Scared that Clear can still stand after such a thing, the Yakuza run away, leaving Aoba and Clear in the alleyway.
Aoba worriedly asks if Clear's okay, and then says they need to wash it off quickly. Clear simply replies that he's okay. Aoba disagrees, saying there are still flames, and they need to wash it off. Clear, again, simply replies that he's okay. Aoba says it's not the time to do stuff like that, and that they need to wash it off. Clear asks if it's an order, says that if it's not an order he won't listen and runs off.
Aoba immediately runs after him, and finds him at a fountain nearby. He slowly approaches him, asking him if he's alright before stating that he was worried. Clear explains that he's washed his head, and he's fine now. Aoba walks closer and finds Clear's still wearing his gas mask, avoiding looking towards Aoba. He asks why, and, sceptical Clear's okay, asks if he's really alright. Clear says he's fine again, and, when Aoba asks why he won't take his mask off, that he'll wash his face later. Aoba pesters him, asking why he won't take his mask off if it doesn't hurt, worried he's lying as to not worry Aoba.
Clear then explains that he was told by his grandpa that he should never remove his mask, to which Aoba asks why. Clear hesitantly explains that his grandpa told him he was different from other people, that his face wasn't like that of a normal person's and he's scared of showing it to Aoba, because Aoba might think he looks like a monster and hate him. Aoba says he wouldn't hate Clear for his face, to which Clear asks how he'd know that. Aoba explains that he wouldn't hate it, because he's stayed with Clear this long for who he is, not what his face looks like, which is why he couldn't hate Clear for his face. He says that even though Clear's strange and a scatterbrain, and even if he does stupid things, he doesn't hate him and never has.
Clear asks Aoba if he's telling the truth, to which Aoba says he is. He asks if Aoba would truly never hate him, not matter what kind of face he has, and Aoba, again, says yes. He asks if he can believe Aoba, to which, for the last time, Aoba says yes. Clear slowly stands, saying he believes in and trusts Aoba, and reaches for his gas mask, and slowly takes it off.
Aoba stares at him for a few moments, amazed that he hasn't been injured by the acid. He then wonders why Clear thought his face wasn't normal, when it's actually rather handsome. Clear mistakes the look on Aoba's face for one of terror, rather than surprise, and says that he must really be hideous after all. Aoba tells him he's wrong, that it's not strange at all. Clear asks if his face is good, to which Aoba is confused. Clear clarifies by asking if his face is just as good as Aoba's. Rather than answer with words, Aoba places a hand on Clear's face, and tells him it's alright. He explains that Clear has the same sort of eyes, mouth and nose as he does, while tracing the lines of his face with his fingertips. Clear asks again if it's really true, and Aoba tells him he is. Clear hesitantly brings his hands up to Aoba's face and begins tracing his features like Aoba is to Clear.
Clear's eyes become watery, and he asks Aoba to say that they look the same again. Aoba repeats it, assuring Clear that there's nothing strange or bad about his face at all. Clear thanks him, almost in tears, and sits down. Aoba tells him to wash his face just in case, and Clear does so. Aoba wonders how Clear's not hurt, and then thinks that maybe, just maybe, Clear isn't human. The two then head back to Glitter.
The next day, Aoba wakes up to Clear - with his gas mask on - leaning over him, watching him as he sleeps. Aoba freaks out and opens his eyes completely, looking at Clear rather startled. Clear simply says good morning and leaves.
When Aoba arrives in the kitchen, he finds Clear has yet again made him breakfast; this time, just some simple toast and salad.
- When Aoba uses Scrap on Clear, he is confronted by two choices: "It's fine to rest" and "It's better to stop now.". If the player stalls for a few seconds between choosing, both will begin to slowly break apart. Since both choices are giving up, Aoba leaves them to crack, having Clear choose for himself, and they eventually shatter (meaning that both options are incorrect and if chosen, it will lead to the bad ending).
- Clear is then able to successfully sing a powerful version of the Jellyfish Song which renders both α and α2 helpless and unable to continue fighting. Toue manages to escape, yet Oval Tower begins to suffer serious damage and begins to crumble (which Clear explains is the original source of their power shutting down). Aoba manages to drag Clear and himself out to safety and eventually makes it back to Glitter. Aoba struggles to find a way to fix Clear immediately and is visibly upset by Clear's condition. However, Clear stops him, saying that since his key lock was destroyed, it was only a matter of time before his body began shutting down. Aoba refuses to believe this, but Clear begs him to listen to his first and last request.
- Clear asks if he could "touch" Aoba, which surprises him, but understands what Clear means and eventually accepts knowing that this is what Clear truly wants. This leads to the two having sex and Aoba discovers that Clear's body reacts the same way as a human's does. The strain on his body causes Clear to break apart little by little before Aoba's eyes, who is powerless to stop this from happening. Aoba insists that they should stop, but Clear refuses. They continue, Aoba being as careful as possible. Before shutting down completely, Clear asks if he had been able to touch Aoba in a way that a human would, to which Aoba affirms through tears, and that to Aoba, Clear was always human, more than anyone.
Clear once more confesses his love for Aoba and thanks him for fulfilling his last wish. As he shuts down, Aoba is left alone, crying in despair.
- Soon after, Aoba manages to bring Clear's body back to the Old Resident's District and desperately tries to fix Clear in secret. He constantly shuts himself away in his room and even took an extended leave from work in order to do so. Tae eventually finds out and Aoba confesses to what he's been doing. She is surprised at first, but understands, saying she knows someone who may be able to fix Clear. This overjoys Aoba, making him happy for the first time ever since Clear's "death".
- A whole year passes as Clear is undergoing repairs, so Aoba returns to work and tries to regain a normal routine. He still painfully misses Clear and is reminded of how they first met when Clear fell from the sky outside of Heibon. After he has finished work for the day, Aoba returns home to an empty house and goes straight to his bedroom. He suddenly hears a familiar song and rushes out onto the balcony in order to hear better. He searches around until his eyes fall upon the back of a familiar figure and the singing finally stops.
- Clear turns around from where he is seated underneath his umbrella upon a nearby rooftop and smiles at Aoba, saying that he had come back to him.
- (If the player chooses either choice without letting them shatter, they will get the bad end.)
- When using Scrap, Aoba ends up sending the wrong messages to Clear, telling him that "It's fine to rest." and/or that "It's better to stop now.". Although it looks as if Clear is able to turn the tables on α and α2, he fails and short-circuits, resulting in Toue becoming bored with the fight, motioning α2 to take Aoba away while he looks on helplessly.
- Aoba is left in a somewhat catatonic state, while being experimented on by Toue's personnel while a young man in white looks on from behind the glass. Aoba can't hear or see him very well, but he recognizes them as Clear and falls asleep.
- Aoba is shown again, this time chained up in a cell-like room. He narrates that he can't see or feel anything anymore and the camera later pans out to reveal that his legs have been cut off from above the knee-down. Aoba is shown to be wearing nothing but a blindfold and it's revealed that, along with his legs, his eyes and vocal chords were also removed; along with his sense of touch. Clear comes in shortly afterwards and begins to affectionately touch Aoba, claiming that he wants him to become like a doll, explaining that dolls don't need limbs or a voice or to see and feel. He then goes on to say that he loves him even more the way he is now.
- It is explained that Clear was reprogrammed by Toue after Scrap had failed, back into his original state. Clear's personality is now completely changed from what it was before - he's possessive and has a twisted view of what love is. Despite Clear turning him into nothing but a lifeless doll for his own amusement, Aoba says that he doesn't care anymore. That to a person like him, who can't move at all, Clear is his entire world.. As long as Clear is happy then he doesn't need to care about anything else.
- The final shot shows Clear biting into Aoba's arm while licking the blood off, whispering how Aoba will soon be as beautiful as he wished him to be. However, before the end credits begin, Clear whispers Aoba's name in a tearful voice which suggests that he might've regained his memories about what they once were before any of this happened.
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- Clear is shown at the beginning of the first episode, appearing to be looking downward in silence as Aoba narrates. Although he does not make much of an appearance, he is given a proper introduction in the second, after he bings Aoba to Heibon safely, following a Rhyme drive-by.