Shin Seiki EVANGELION: Tamashii no Refuran/ Neon Genesis EVANGELION Soul Refrain

Refrain; Vulgar Latin refringere, and later from Old French refraindre "to repeat",

Prologue: Ankoku (Darkness)

Ebbing and flowing…. ebbing and flowing….


The smell of blood….

Silence… Deafening Silence

'Am I still in Unit 01?'

Ikari Shinji peeled open his eyelids, his vision blurred at first, as if from lack of use, then slowly focusing. he realized he was no longer in the entry Plug of Evangelion Unit 01. An orange sea stretched for endless miles all around, the waves undulating beneath him, and the sky was stained a color of crimson not unlike that of blood. Beyond that the moon sat very low in the endless black expanse of the sky, like a giant white pearl set upon the blackest satin, the void beyond it dotted with millions of tiny stars.

The overwhelming scent of LCL constantly assaulted his nostrils, the metallic scent of blood, so strong that he could taste. Around him the breaking waves the only sound to shatter the eerie silence. It was then he also realized that he was half submerged in the aforementioned orangish sea and that the nude form of Ayanami Rei was mounted atop him in a very peculiar position. Had this poor coward not single handedly caused the destruction of the entire human race, he might have found this erotic, to say nothing of his attraction to the blue haired beauty that was straddled atop him.

But Shinji had a hard time feeling anything at the moment, his body feeling as if it both existed and did not exist. His mind feeling as if he had been dreaming for untold ages, the lines between a dream and reality blurring and melding. He could remember fragments of other worlds, other lifetimes, that he was sure were not his own. The harder he tried to focus on those fleeting fragments, the quicker they slipped away.

Was this a dream? Was it reality?

He felt both whole and empty at the same time, and this scared him. He felt violated, as if every little thing he had done in life was laid bare for all to see, 0.

'Am I... dead?'

Indeed, death would explain this current situation as the last thing he could coherently remember was being in Unit-01 surrounded by the Mass Production EVA Series. He could recall fragments of seeing Rei, Asuka, Misato, and Kaworu and then nothingness.

Rei... he had tried so hard to save her against the Sixteenth Angel, he stood there, dumbfounded as that foul creature violated her. Ayanami Rei, this beautiful girl, whom through no fault of her own had been a pawn in this from the start. She had given everything to make sure he survived, right from the beginning. He looked into the eyes of the young woman looking down at him, hoping to find even a glimmer of an answer there.

"Ayanami... Where are we?"

"This is the sea of LCL, the sea of the origin of life. This is a world without A.T Fields and therefore without your own shape, where individual forms do not exist. You cannot tell the difference between one person or another. An ambiguous world. Everything is yourself, and also not yourself. A dead world."

"I died?"

"Not quite. Everything has combined into one. This is the world you've been hoping for. It is like this."

'No one wants me so they can all just die!'

'I did this… ?

'No one cares whether or not I exist. Nothing ever changes, so they can all just die.'

'No… this is isn't… 'This isn't right, it feels wrong.'

"But... This isn't it. I don't believe this is it..."

'I didn't know this would happen…. All I wanted… '

The horrible truth of his role in Third Impact dawned upon Shinji, in his desire for a place where he could not be hurt, he had influenced these events, created a world where there was no self, without shape, without individuality. But this wasn't what he wanted. Existing in a place between life and death was worse than never existing at all.

"If you hope that other people exist again, your heart with separate everyone once more. But you will be frightened of other people again."

Shinji pondered this for a moment, absorbing the enormity of the consequences. People would feel fear again, but they would have a choice. Their fate would be their own. He pulled Rei's hands from his chest and took her hand in his.

"It doesn't matter, thank you. "

The orange luminescence of that place shifted serenely to a calming blue, and Shinji felt the emptiness within himself dissipate. He laid his head upon Rei's lap, his fingers still entwined around the cross that Misato had given him. Shinji wasn't sure that this was the Ayanami Rei he knew, but for now, it was enough to calmly lay there.

"I felt that there are only hateful things there. I thought it was alright to run away. But there was nothing good in that place I escaped to, either. Because I didn't exist there, and so no one existed."

A new voice joined them, one that Shinji had never expected to hear again.

"Produce the A.T Field once more... Is it alright for it to cause you and others pain again?"

Shinji looked up from his resting place on Rei's lap, Nagisa Kaworu standing over both of them, his face graced with that innocent warm smile. Shinji sat up and blinked several times to convince himself that the Fifth Children was standing there in the flesh. Kaworu, whom had been killed by his own hands, the only person whom had ever told him he was loved. In the short time he had known the Fifth Children, he found in him a kindred spirit, someone whom he didn't have to prove his worth to. Nagisa Kaworu had been the closest thing to a brother that Shinji had in those closing days. He could confide in Kaworu, without fear of judgement, like he felt he never could with anyone else.

"Kaworu-kun? How?"

"What if I told you, there was another choice?"

A look of utter confusion crossed Shinji's face, and Kaworu knew that he could proceed. He had watched Shinji create and dismiss many possibilities, different worlds, whole lifetimes, rejecting each one in turn, eradicating them from his mind. Each one moving further and further from his reality. But none held the answers he had been seeking. Kaworu had no delusions how this would end for his cherished friend if things continued this way, he had seen it. A world devoid of life, where those who emerged would face a constant struggle to survive, people clinging to life in a dead world.

'A life that Shinji-kun will not survive.'

He looked from his friend to the young woman who sat behind him. He understood her motives, why she had done what she had, handing the reigns of Instrumentality to the young Ikari. To Rei, it was the only way she felt she could help him find the happiness he sought for so long. It was an act of love. Kaworu's smile widened as he realized Shinji didn't quite understand her motives. These two had such love for each other, and neither of them knew quite how to express it. Shinji, because he felt nothing but hate for himself, therefore felt unworthy to love others.

'I can give you a chance at happiness, Shinji-kun. But you must make the choice, my dearest friend'

"What if I told you there was a way that no one had to be hurt. That I could give you another chance to save those most important to you?"

Shinji's eyes went wide, his mind analyzing what his dearest friend had said. Kaworu had made it sound like he could send him back to before Third Impact. But that made no sense.

"What do you mean Kaworu? What are you saying?"

"I'm telling you that you can return to that day."

"What for? I'll only push everyone away again."

Shinji cast his eyes downward, just because he had no desire to consign all of humanity to oblivion, didn't mean he wished to suffer their rejection again. Kaworu sighed, and knelt by his friend, offering him his hand. He knew that Shinji wouldn't desire the world to come, but his nature paralyzed him and would hinder him in this endeavor. Kaworu knew that Shinji held all the answers he sought, he just had to make Shinji see them himself.

"Come with me Shinji-kun, I have something to show you."

Hesitantly, Shinji reached up and took Kaworu's hand. When the two hands clasped, Shinji was thrown back to that day, the day Ikari Gendou had abandoned his son. Shinji observed the scene with a hateful fire in his eyes. A young boy crying for the father whom was leaving him behind. Shinji clenched and unclenched his fist, the rage building up with in him, only for a smaller hand to take his. His head jerked to the side to see Rei, in her school uniform, looking at him, the slightest hint of sadness in her features. Shinji heard a light chuckle from Kaworu as he approached them from behind.

"From this moment, your life could have gone any number of directions. For you though, the loss of both your mother and father at such a young age broke your spirit."

"I began to think it was my fault. That Father left me because it was my fault Mother died. I pleaded with him to stay, swore I'd be a good boy, but he just walked away. I started to be afraid that anyone I became close to and everyone I loved would die or leave me. Then when he called me to Tokyo-3, I wanted… I wanted to tell him I hate him.

"But you don't hate him do you, Shinji-kun?"

Shinji watched as his surroundings changed again, this time to a playground or park with a lone child sitting on the swing. Another child, bigger than the first, a little overweight, approached the boy on the swing. Shinji knew this memory, it was one that he had buried in the depths of his mind, one from his early childhood. The boy on the swing was Shinji himself, who even at the young age of six had adapted the outlook that would define most of his life.

'Yo, Ikari! You're on my swing.'

'There are other swings, Keitaro.'

'Yeah, those are mine too. Now get off.'

The little boy quickly removed himself from the swing, staring intently down at the ground. He didn't want any trouble, and Keitaro already picked on him enough in school. He started to walk away when he heard the bully speak up again.

'Yo, Ikari. I heard that your Dad killed your mom.'

The young Shinji stopped in his tracks, and started shaking. The bully smirked with a mean intent behind his words.

'What does that even feel like being the kid of someone who killed your mom?'

'That's not true. Dad loved my mom.'

'Yeah well my dad told me that he killed her, and he don't lie to me'

'He didn't.'

'Did so.'


Shinji watched as his younger self launched himself at the bully, fists flying, flesh hitting flesh. He had broken Keitaro's nose that day, and the bully had also needed twenty-six stitches. Shinji himself had been yelled at by his teacher for hours afterward, and been punished for many weeks.

"He said my father killed my mother, but he didn't. I knew he didn't. Father loved mother more than anything, and that's why I knew he couldn't have done those awful things everyone said. But my teacher didn't understand. He told me that no matter what I couldn't fight."

"And so you didn't from that day forward, but in the back of your mind, you always knew that your father loved your mother, even if your surface mind buried it."

"Maybe that's why I couldn't hate him, even after he made me hurt Touji, and after I found out what he did to Ayanami. Somewhere in my mind, I knew I wanted to connect with my father again, to show him that I could be the son he wanted, a son he could be proud of."

Kaworu nodded, he knew seeing these memories again like this was hard for Shinji, but time was running short. He could feel the gestalt being that humanity had become begin to deteriorate, and with it, Shinji's chance at happiness.

"But at the same time your fears took hold of you, didn't they, Shinji-kun. Instead of fighting you started running. You pushed everyone away, even though what you really desired was the closeness of others. While you desired lasting relationships, your fears kept you from forging close bonds with anyone. You became a coward, your fondest wish became your deepest fear."

Shinji nodded, Kaworu spoke the hidden truth of his heart, forcing these memories kept in the dark of his mind back into the light. Kaworu knew that Shinji was beginning to understand himself, that his hidden strength was there all along. He looked to Rei, whom understood his intent and she, through her will, changed their surroundings once more. This time to the depths of Nerv, the Terminal Dogma, where the commander and Rei herself stood before the titanic form of the Second Angel; Lilith, the entirety of the cavern shaking from the events unfolding high above. Shinji watched in awe of these events, not quite understanding what was transpiring.

'It appears to have begun. Now, Rei, it's time to reunite me with Yui once more.'

Rei slowly lifted her gaze to the Commander's face.

'I am not your doll.'

Shinji watched as Rei rejected his father despite his pleas, saying that Shinji himself that he was calling to her. Shocked, Shinji turned his gaze to Rei once more, as she in return tightened her grasp on his hand though she could not bring her eyes to meet his.

"Ayanami… why? Why would you do that?"

Kaworu put his hand on Shinji's shoulder, smiling knowingly at his cherished friend. Shinji turned back to Kaworu, a quizzical look crossing his face.

"Isn't it obvious, Shinji-kun? It was an act of love, Rei-chan wanted your happiness above all, and this was the only way she saw she could offer you that."

"Are you saying…?"

"I'm saying she loves you."

Shinji felt as if he had been pierced through the heart, he staggered backward, releasing Rei's hand, falling to his knees. He had not known, had never known. He felt he was a loathsome creature undeserving of anyone's love, how could it be that Rei could have loved him? Kaworu dismissed the scene within the Terminal Dogma with a wave of his hand before again kneeling by Shinji.

"Is it so outlandish to consider, Shinji-kun? Would it surprise you to know that many of those you connected with had thoughts of you before the collecting of souls? Like Suzuhara-kun"

Piercing the silence in the darkness surrounding them, Shinji could here his friend Touji's voice/

"Shinji, I know you can't hear me, but I don't blame you, never did. It ain't your fault that Angel got me. Just wish I could have been out there, with you and Soryu and Ayanami"


"Shinji, if anyone can save us, its you."

"Even your father's final thoughts were of you."


"When Shinji is near me, all I ever do is cause him pain. It was better when I did nothing at all. I didn't believe anyone could love me. This is my retribution. Forgive me, Shinji."

"You see Shinji-kun, they all believed in you, even when you didn't They all knew you had the strength. Even your father."

The rage that had been boiling up within Shinji finally reached its breaking point. He shot up right, and grabbed Kaworu by his shirt. The vessel of Adam's soul couldn't help but smirk as he witnessed the strength he had known was with Ikari Shinji finally manifesting itself. Were he a Lilin, he may have been afraid of such fire, but in truth he had been making an effort to draw out the fire rising within Ikari Shinji.

"Strength?! What strength, do I have?! I'm just a coward who can't do anything right!"

Rei's soft voice filled Shinji's ears.

"That is not true, Ikari-kun"

Shinji whipped his head around to face Rei again.

"If I was so strong, I wouldn't have run away from Misato-san, even though all she ever did was try to help me! I wouldn't have done a terrible thing to Asuka and then let her die! When the fifth angel attacked, you risked your life to ensure my safety. If I had such strength, you wouldn't have had to. If I had reacted when Touji's EVA was taken over by an angel I could have saved him. Where was my strength then? When the fourteenth angel attacked if I had been there at first you wouldn't have gone after it with that N2 Mine. When the sixteenth Angel attacked, if only I had moved even a little faster, I could have... I could have saved you. But I let you die too, all because I'm a weakling and a coward!"

Shinji released Kaworu shirt sinking back to his knees with ragged breaths. Kaworu stood, hands in his pockets, unfazed by Shinji's denials, his smile widening as he saw the very strength that Shinji himself was denying.

"When you took fault for injuring Suzuhara-kun, you were willing to pass judgement on those you perceived to be the cause and When you saw what the fourteenth Angel had done to Soryu-san and Rei-chan's Evangelions, you cast away your own desires and once again piloted Unit-01. And in a time of crisis, what else could you call that but strength? These are but a few instances where your true strength shined through."

"But I-"

"You have the strength..."

Kaworu touched his index and middle fingers over Shinji's heart.

"...Here. You must let go of your weakness."

Shinji stared at the ground, he could feel something shifting within himself, as if pieces of a puzzle deep in his mind and his heart were starting to fall into their proper place. He looked at Kaworu and asked the deciding question;

"What happens if I don't."

Kaworu sighed, he had been expecting the question, but he had hoped he could spare Shinji the answer.

"I'll show you."

The darkness faded to become a desolate wasteland, stained red. Rei and Shinji stood beside Kaworu on a cliff overhanging the beach with water the color of blood lapping at the shore. Shinji's eyes widened in horror as he witnessed himself attempting to strangle Asuka.

"You won't succeed this time, but in a few days' time, Soryu-san will mention Rei-chan negatively, and... Well it doesn't end well for her. All alone, swallowed by despair and loneliness, you will drown yourself several days later."

Shinji felt if he'd been slapped in the face by the truth, as if his innermost desires had been laid bare for all to see.

"I kill Asuka... over Rei?"

Kaworu shook his head, locking eyes with Rei.

"When one loves someone, they are capable of many things they might otherwise never do. Love is irrational, and many times, we never even notice it's there until it's too late."

Shinji opened his mouth, as if to debate the words that Kaworu had spoken, only to find that he could not. What was it that his mother had said?

'This is the Ayanami Rei that is inside your heart.'

"Do you still try to fool yourself otherwise? Soryu-san and Katsuragi-san were indeed beautiful, and you did care for them in your own way, and they you. However, I watched as you created worlds and lifetimes, each shaping themselves to your perceived wishes, and in those which you pursued a relationship with Soryu-san, you had to change her personality, she became an entirely different individual than the actual Soryu-san. The same can be said of Katsuragi-san, in the worlds where you pursued consider your actions with Rei-chan. When the Fifth lie slain by your hand your first concern was Rei-chan's safety. You could have easily waited for others to attend to her and her Evangelion but you took it upon yourself to ensure she was alive, I believe your hands were burnt quite severely even through your plugsuit, were they not?"

Shinji knew he couldn't deny that, he had been lucky in that he bore no scars as his father did. Not that he would have cared, he had to make sure Rei was alright after enduring the fifth Angel's particle beam. He hadn't thought for a moment of his own safety.

"And have you considered why Lilith took the shape of Rei-chan and I? At that point the mother of Lilin could have assumed any shape she wished, and yet she chose to appear to you as Rei-chan and I. Why not as Soryu-san? Or Katsuragi-san? Or even your mother?"

Shinji's mind fumbled around for an answer, how could he be expected to understand such a thing as the motives of Lilith?

"I...I don't know."

"You and Rei-chan have a bond, one that neither of you realized or would allow yourselves to admit. She is one of the few you truly let inside your heart, even if you never realized it, and that is how she knew you were calling to her, perhaps not with words, but with your heart."

It pained Kaworu to see Shinji as he was, knowing the young man deserved so much more than he had been given, but their time was nearly up.

"Shinji-kun, I love you like my own flesh and I know this is not easy, but I can only guide you, the decision must be yours. So, I ask you, Ikari Shinji-kun, does everyone, Rei-chan included, die, or do you set the world as it should have been?"

"But How?! How Am I supposed to save the world?! When the sixteenth angel attacked I couldn't...I couldn't even save...Rei."

Tears streaked down Shinji's cheeks, collecting upon the ground.

"You can change that Ikari-kun."

Rei knelt beside Shinji, placing her hand over his as Kaworu continued.

"The first step of every Journey takes incredible courage, and you've taken those steps, my dear friend. "

Shinji stared at the stained earth, his mind racing. Did he truly love Rei? He liked her, but did he love her? Would he die for her? The deeper he looked within himself he saw all the little things that provided his answer. All the times he thought of her, the little interactions between them, a small smile, a quiet thank you, and he remembered the indescribable pain when she and EVA 00 self-destructed in her effort to save him from the sixteenth, a sacrifice that robbed him of his tears. Even as far back as the battle with the fifth angel, when he blindly rushed to pry the hatch from the superheated Unit-00 entry plug.

He'd knew he'd be willing to give his life, so Rei could live. And that she would do, and had done, the same for him.

Shinji stroked Rei's cheek with his right hand, she closed her eyes and leaned into his caress. Such close contact, it was Shinji's deepest desire, and his biggest fear. A smile spread across his lips as he understood now what his father felt for his mother. As the final tear fell, Shinji realized that he wasn't afraid anymore. For the first time in his life Shinji felt his heart filled with unbelievable strength. He knew what had to be done.

Kaworu smiled.

'He is ready.'

"It's not as hard as it seems, is it, Shinji-kun?"

Shinji stood once more, looked to Kaworu, and the vessel of Adam's soul smiled brightly.

"What did you do to me?"

"As I said, you have had the strength with in you all along, I merely guided you through the journey to see that yourself. Whether you stay on that path is up to you."

"If I go back, I have a chance save everyone; Rei? Misato? Asuka? My Father?"


"Will I still have my memories? This would all be pointless without them."


"Then the choice is simple; There is no choice. I won't watch them die again. I'm tired of running. I mustn't run away. I can't run away. I won't run away."

"Then it is settled. We will send you back to the day it began. The fate of the Lilin… No, humanity is in your hands, Shinji-kun. But be aware, there will be a long road filled with hardships before you now, this endeavor is not without consequence."

"I don't care, I have to do it."

Kaworu nodded, smiling broadly.

"I thought you'd say that."

Shinji-began to feel himself drift away; literally pulled away from the ground, Rei and Kaworu smiling after him

"Good bye, Shinji-kun, maybe this time we can love each other like we were meant to."

"Hey, I almost forgot to tell you; You're welcome for the gift, sayanora Shinji-niisan!"

As his blinding light consumed his vision, Shinji was allowed a final thought;

'What gift?'

-New Tokyo-3, 2015-

"Due to the present state of emergency, all phone lines have been disabled"

Shinji blinked once and found himself holding the green receiver of a payphone. He cautiously looked around, taking in his surroundings. The structures, the vehicles, the air itself. This wasn't a trick of the mind. Everything was as it had been, the very day he arrived in Tokyo-3. He slammed the phone down, his eyes alight with determination. Ikari Shinji's soul was burning with a fire he had never known before. He knew what he had to do. He would have his own scenario, and he would do it right.

"I have to, for you, Rei, and for everyone"



Tengoku no Kioku {Memories of Heaven} as sung by Hayashibara Megumi -from the Album Neon Genesis Evangelion DECADE

(Used from the opening sequence to the Memory Sequences)

Infantile Dependence, Adult Dependency by Sagisu Shiro from the Album Neon Genesis Evangelion OST Vol. III

(Used from Memory Sequences to when Shinji recalls Yui's words during Impact)

Heisoku no Kakudai (Expansion of Blockade) by Sagisu Shiro from the Album The End of Evangelion OST

(Used from Recalling Yui's words to being sent back)

Tamashii no Refuran (Soul Refrain) as sung by Takahashi Yoko from the Ablum Refrain of Evangelion

(Aside from being what could be considered the "main theme" of the fic, this was used once Shinji arrives back on Day 1)

Author's Notes


This rewrite has been a long time coming, and I'm glad I finally found the will to start it again. I apologize to my audience for making you all wait this long to continue work on this. I began this project with the intention of writing a simple story that allowed Shinji a second chance, with a little bit of Shinji x Rei goodness added. It became something far more, the more I immersed myself in this work. With a wealth of supplemental information and extra-canonical materials, the Rebuilds, and the Manga, I saw the potential for something truly special.

As you may or may not have guessed the title is derived from a track on the Neon Genesis Evangelion: Death and Rebirth Soundtrack, "Tamashii no Refuran" or in English "Soul's Refrain." If you haven't heard it, I strongly suggest you do, as it and its various remixes are wonderful pieces of music, and with today's technology you could easily find them on the internet. The Title was important for a single significant reason, and that is that this is a "Restart" story. Equal parts "fix-fic", "rebuild fic" & "Peggy-sue".

That being said, this is not my first Evangelion Fanfiction, in fact it's my third. The first one was an ill-fated attempt in my late teens I called NGE 0, it was horribly written with no sense of pacing and the characters were OOC straight out of the box. As you can imagine, I abandoned it pretty early on. The next attempt was a few years later, a sort of continuation/sequel called Neon Genesis Armageddon. This attempt fared better, I had seen the series several times by this point and I had a decent grasp on the characters. So, with few exceptions most of the characters were in-character with the show. Amusingly enough I came up with several concepts that I later found out were introduced in Neon Genesis Evangelion: ANIMA, which was produced around the same time. NGA came to a screeching halt however when the computer that I was writing it on suffered a system failure, perhaps someday I might decide to rewrite it and post it. I bring up NGA because I am borrowing a few ideas from that earlier work to be used in this one.

I am NOT Anno Hideaki, or Sadamoto Yoshiyuki, as it should come as no surprise to all of you, this is not a faithful recreation of Neon Genesis Evangelion TV series, manga, or the Rebuild of Evangelion Movies. In fact, the only time I use verbatim dialogue from the scripts of those works is when the situation calls for it. Thusly, it can be said that Soul Refrain plays by its own rules, while using the ruleset of the TV show as a guide. Soul Refrain in many ways follows its own canon, blending in elements of many of the supplemental materials, spin-offs, non-canon games, and so-on. I've done meticulous research for this work, including repeated viewing of all 26 TV episodes and End of Evangelion and the three Rebuild of Evangelion movies. I've examined many of the currently available translations and discussions regarding the expanded universe material, such as Neon Genesis Evangelion ANIMA and Neon Genesis Evangelion 2: Evangelions (The Videogame for the PS2 and PSP) as well as the not-so-canon materials such as Neon Genesis Evangelion Kotetsu no Girlfriend 1 & 2. Characters from these various works may appear in some form within Soul Refrain. I must extend my thanks to the Evageeks Community (in particular the user Reichu's work with The Kimitsu Jouhou from NGE2 and user TMBounty_Hunter for his collecting of NGE: A raws). I also extend my thanks to my audience, for their reviews; both praise and constructive criticism, and of course their patience. Moving forward, the Author's Notes following each chapter, will be shorter in length, and will address each specific chapter.