Insert the usual legal mumbo jumbo here. Neon Genesis Evangelion is the intellectual property of its owners and creators, etc and so forth. I do not own, nor claim to own, the characters and ideas brought forth in this story.
Gone…everything was gone. All the people that he had, save for Asuka, were gone from his life and probably forever knowing his luck. Sitting upon a small chunk of concrete, the weary adolescent stared out at the glowing sea before him…wondering if what he had done was the right decision. He had left Asuka alone to talk a walk down the shoreline, hoping to air out his thoughts before going back to his friend. She still had not said much to him, save for a few words expressing what she was feeling at that moment – usually just complaining about being hungry.
"I've probably screwed myself for life," Shinji grumbled to himself as he rested his chin on his palms.
"Do you honestly believe that?" An unknown voice suddenly spoke up from right beside Shinji, startling the boy right off his seat. His eyes widened in disbelief as he saw what was suddenly standing next to the concrete block next to him. It wasn't human, that's for certain, as its body appeared to be nothing more than a dense, transparent, black, swirling mass in the shape of a humanoid figure. Two single points of glowing white light, which Shinji assumed were eyes, gazed down upon the bewildered child who wasn't sure if he had lost his sanity or had fallen asleep now.
"Who are you…more importantly, what are you?" Shinji answered, juggling between deciding whether what he saw was real or he was actually just asleep on the beach somewhere.
"Something a bit beyond your comprehension child," it answered. Its voice, neither distinctly male nor female, carried an oddly reassuring tone with it, bringing a slight calming effect to poor Shinji.
"I'm dead aren't I? Asuka murdered me in my sleep, didn't she?"
The being before him chuckled lightly before shaking its head. "No, you are very much alive. Though how long you'll last out in this barren land is another question altogether." Shinji remained silent at first, not quite sure what to make of what the being was telling him. It did have a point. He may have lived alone a great deal but he had little idea how to fend for himself to such an extreme degree. It had been almost a day since Shinji found himself on the beach with Asuka, they hadn't eaten anything since then.
"What do you want?"
"I bring a proposal to you child. You have proven to be a…champion to humanity of sorts. You have survived terrible odds and have prevailed…to a degree. Though, whether or not this is victory is yet another question that cannot be answered." Obviously, the being referred to the merging of souls in the golden sea that stretched out to the horizon. "Can you hear it, Shinji Ikari? Their voices…hundreds of millions of souls merged into one being. Try as you might, one can never truly take out the individuality of humanity. It will always exist. It's simply a matter of form."
"Um…what are you getting at?" Confusion didn't begin to describe what Shinji was feeling at the moment.
"What if I gave you the opportunity to undo all this?"
"Yes by changing the choices made."
"Or we can just repeat everything I say and this conversation can take twice as long."
"An outcome is guided by the choices of mortal men and women Mr. Ikari. For every decision there are a hundred outcomes, which lead to a hundred new decisions with their own one hundred outcomes. I am presenting you the option, Ikari, to have some of those choices changed as to create a new outcome to this…ordeal."
Shinji continued with his puzzled stare. Perhaps the hunger had gotten to him and he was now hallucinating. "What sort of changes are we talking about?"
"For starters this," it explained and pointed out to the sea again. "Human Instrumentality can be undone. Tokyo-3 and its inhabitants could walk the world again in their own flesh and blood and you, Ikari, will be among your peers again – Horaki, Aida, Suzuhara…Ayanami."
"You can bring Rei back?" Shinji jumped back to his feet at the mention of her name.
"I just said I can undo Instrumentality. She falls into that category."
"What about Misato? Can you bring her back too?"
"Katsuragi died by mortal hands. I can't guarantee that I can undo her death."
"Fine. Just…do what you can!"
"Settle down child, this isn't the wonder deal that it might seem like," the being explained, bringing about a slight sense of worry from Shinji. "Every decision brings about a good and a bad – that is the nature of the world. When good is done in the world, inevitably something bad happens elsewhere. It is a balance between good and evil that has existed since the beginning of time itself. The Heavens were created and so was hell. Man was created and so was temptation. Love was born and so was despair. Humanity gained freedom and so did it gain the evils of the world. You get where I'm going with this?"
Shinji nodded his head slowly, still not liking where this was going. "So what will happen if you do this?"
"Your fight will not be over. It will not be immediate but you and your friends will likely once again be plunged into an ordeal that will decide the progress of humanity. The exact outcome is unknown even to me – you could forge a new order in the world, wind up back here, or lose everything. If you believe in yourself and those around you…I'm certain that you will prevail."
All the confusion and worry had faded away from Shinji as he was faced with this monumental decision. What had sounded too good to be true had become a moral dilemma. Both decisions had an uncertain outcome…but he wanted to see her again.
"I want you to undo Instrumentality," Shinji finally answered after a long pause of deep thought. "Why are you doing this anyways?"
For once, the being didn't answer right away, apparently not having an answer already for this question. "I believe some poor choices were made that should not have been. There will be a time where humanity will become like what it is you see before you, but now is not that time. It was not a decision for humans to make just yet – you are not ready for such a state of existence. This…is not right."
"Are you…God or something?"
"No - God rarely interacts directly with humanity nor would he be limited by time like I am. I can only present this opportunity to you for a short time. Now please shut your eyes." Shinji silently obeyed. "When you open them again, you'll retain your knowledge of what happened here today but you are not to speak of this decision you've made to anybody. We will meet again in your new world but I will not be able to provide much more than encouraging words for you. Never lose faith in yourself Shinji and always remember that your friends will be there for you."
Everything fell silent for a brief time. A strange, almost pleasant breeze seemed to blow past Shinji, rustling his hair for a moment. He felt cold for a moment and then slightly disorientated. Numbness spread through his body that lasted no longer than the earlier breeze and at long last, Shinji felt himself in a different location and position. He could hear computerized beeps and indistinct chatter in the background. Had it actually been done? For some reason, Shinji felt exceptionally drowsy and his once active eyelids felt like they weighed a tonne. Eventually, he pried them open and found himself staring at the white acoustic-tiled ceiling of a hospital. What confused him the most was the odd pressure on his abdomen.
However, that confusion was only momentary as he saw the unconscious form of the redheaded teenager, Asuka, laying her head on his stomach as she slept peacefully.
"Asuka?" Shinji blurted in confusion.
Immediately, the girl began to stir in her sleep, slowly drifting back to the conscious world. Those cerulean eyes gazed at him in amazement for a second before she sprang back to an upright position in her chair. "Shinji! Thank god you're awake!"
"You've been in a coma for nearly a month."