This is a remake of a story I wrote when I was much younger, this novel depicts what may have happened if Shinji would have woke up next to Rei instead of Asuka on the beach after Third Impact. I, as always, do not own any of the material in this story, I do not own the characters, objects, or fictitious events, they are all property of Gainax. I hope you enjoy this prologue chapter, and I hope for a multitude of good and bad reviews. Thank you.

A Boy, a Doll, and the End of the World

"Asuka, oh God, Asuka. Shinji, Asuka is, she's...

"We have begun Third Impact"

"Kawou? Is that you?"

"I wish everyone would just die!"

"Then tell me, what is your heart for?"

"Please, someone help me...please." "...no."

Prologue Chapter

Assessment of the Current Situation

All I see is blood. The blood Shinji saw right before everything went dark, it's the same blood he sees now. It covered him completely, he was practically drowning in it. But this was different, his mind echoed, these were the first thoughts he had since he regained consciousness. The blood was thinner, and every time his heart beat, a plethora of veins appeared for a split second then disappeared alongside a thunderous headache. I must be dead. Shinji thought, his mind started to become less scattered. For a moment, he was happy, his death made it simple for him to escape, he didn't have to face those he hurt or failed, but as his senses slowly came back to him a welling inside his stomach grew, for he knew he was not dead. This realization came when his right hand began itch because of the small grains of sand that found their way in between his fingers.

"Uggnnn…" He heard a feminine voice groan beside him, and with that came the immediate sound of waves crashing against the shore. Shinji's eyes began to water, and he held them closed with every bit of strength he had. The waves were somewhat soothing, and after a few minutes he forgot all the horrors that he had just been put through, and because of his mental exhaustion was on the brink of falling asleep when he heard his name being called from a whisper-like voice.

"Ikari?"

Shinji's head rolled to the side, and his eyes bulged open, ignoring the blinding sun he held them as wide as he could.

There she sat, one of the three most important, but practically only women, in his life. Rei Ayanami, her blue hair almost floating off her forehead, the back, which, because of the water, became a darker shade of blue and was covered in sand. Her unblinking raven eyes stared straight up at the sky, and her albino skin practically reflected all sunlight off her face. She was still wearing her plug suit, a large bandage wrapped around the top of her arm, below it the bandage, the plug suit looked as it had been torn off, and only the skin below her elbow showed through. Breathing slowly, she was patiently awaiting his response, her face, as per usual, showed no sign of emotion.

From the moment Rei had opened her eyes she began to analyze the situation she was in. Quickly she located pilot Ikari, he was breathing fine, the beach where the two were was completely deserted. The cloudless night sky was acceptable because of artificial lights coming from the remains of Tokyo 3's cityscape. Rei positioned herself upright, "I must go to Ikari.", those words echoed in her mind from only a few hours ago. She felt exhausted, though physically not more then five hours had passed since she had merged with Adam, it felt as though a millennium had passed. Rei thought for a moment, she had defied Gendo, her pseudo father, her creator, and her commanding officer, if she was not the link between him and his wife, she would be killed without thought. Wait, Dr. Aikagi…She had destroyed all of her replicas, there would be no more husks, no more spare body parts, and no more Rei Ayanami, she would be free. This caused something inside of her to crack, to change, and because of this, she had to know oneo thing.

"Yes Ayanami?" Shinji replied meekly.

Rei held this silence for an excruciating long time, and right before Shinji was about to repeat himself, she blinked for the very first time, and when her eyes reopened she was staring right into his.

"What number am I?"

At first Shinji didn't know how to reply, after seeing a massive God-Rei stand in front of his Unit-01, he almost forgot that she was a clone. Yet even with remembering this, Shinji still didn't know what to say, honestly he didn't even know why she was here. Closing his eyes he tried to remember what happened last…he was being pulled through a world that felt like a broken record player, jumping to this and that, not really staying in one place for more than a mere split second. For an instant, near the beginning and the end, he felt almost as if he were God, and all existence bowed before him, and in the beginning he was their destroyer, but in the end, their creator. Still believing he had done the right thing in the beginning, slaughtering everyone and casting them each into their own person Heaven, his mind still believed that he should not have to power to control them, and in the end, gave every living creature the power to choose, whether to stay in their own little worlds, or return their birthplace, Earth, a world of pain and suffering. Every creature then made their own decision…except for one. Rei Ayanami, the girl with only a piece of a soul, was not given a home. Without even truly thinking it out, Shinji subconsciously made the decision for Rei to be remade whole. This did nothing but made Shinji feel worse, he had brought her back to a world full of pain, misery, and hate…As Shinji's tears began to well back up he felt Rei sit up beside him, ignoring the sand that still clung to her arms and back. Shinji knew he had to answer her, it was the least he could do.

"You're not a number anymore Ayanami. You…are you."

Shinji felt weird saying this, and was at first worried that she might not understand him, but before he could even try and restate it, Rei practically summed up everything quickly.

"Then I am no longer just a tool of Gendo. I am…whole?"
"Ye…yes." Shinji stuttered, still worried that he had ruined Rei. But wasn't this better than oblivion. No, Shinji looked at her and knew, once again, he had hurt those around him.

Rei turned and looked out over the water, the sky and the water matched her eyes, stone crosses littered the water both sides of her peripheral vision. For a moment she almost jumped when she took in all of what sat in front of her, a giant replica of her own head, it was slowly cracking and deteriorating. And inside Rei felt different, no longer able to control her emotions, they seemed to nearly rip through her mind. Feelings of remorse for her own self that sat sinking in the ocean, feelings of happiness to be whole, and feelings of fear for the world she has been put into, but most of all, a very unfamiliar feeling that she has had ever since Shinji saved her life after they fought off one of the Angels. She felt the warm sun on her skin, the cool smell of salt water, and felt the sands shift as Shinji moved uncomfortably beside her. Analyzing the situation, she felt as though her pros far outweighed the cons of her previous lives, she no longer needed to wish for death, for she was no one's doll anymore.

"This is acceptable."

Shinji felt a slight feeling of relief, Rei seemed somewhat happy with her present situation, well as happy as Rei Ayanami gets, and so he sat up beside her. And for a moment the two of them just stared out at the ocean, listening to the waves crash against the beach. Shinji, thinking about the mess he'd made with the world in his usual self-loathing manner, and Rei, trying to understand everything she'd been given, but more importantly why were they the only two remaining.

"Ikari, where is everyone else?"
Rei didn't entirely care, being alone had been perfectly acceptable, but this lengthened silence between her and Shinji gave her a new odd feeling that she didn't entirely enjoy.

Shinji looked around, up and down the beach, Rei was right, there was no one else here. No Asuka, no Misato, no Gendo…no one. They were alone. Had everyone else decided to stay in their own personal Heavens, or had he somehow failed them and…

"Do not worry, you have done no wrong Shinji Ikari…this is the world you wished for, the one you created. Everyone is happy, and it's all thanks to you. Congratulations."

A familiar male voice spoke to him from inside his head. Shinji jumped, and looked around quickly searching for the voice.

"That voice…" Shinji muttered, it was just like Ka…

"Are you alright?" Rei asked, with a hint of concern on her face. This new feeling of…feeling was confusing to Rei, and instead of thinking every action over thoroughly she felt unable to control her self on certain topics.

"Um…y..yeah Ayanami, I…I don't know where everyone else is…I think they're all…"

Shinji just then caught a glimpse of where humanity stood, the circle of red that surrounded the planet. Each red crystal orb was a human, living all in their own new world.

"…Up there."

Rei looked up and saw what Shinji was speaking of, though she did not quite understand, everything felt familiar, though her own last memory was that of disappearing into Adam, she felt as though she had been a part of all this. Whatever was going on, the feeling of discomfort again overtook her, and she wanted to be anywhere but on this beach.

"May we leave this place?"

"Of…of course…is…are you alright?"

Shinji asked, worrisome.

"Yes, I am fine. But I detest this place."

Detest…Rei felt odd saying this, she had never disliked anything more than a simple annoyance, Rei would not even classify the Second Child as someone she hated, but for whatever reason she was being controlled by her emotions for, they were practically screaming a feeling of hate toward the red water, the crimson sky, and her almost completely collapsed former self.

"Why?" Shinji asked dumbly, interrupting Rei's thoughts.

"Because, it reminds me of your father."