Let's get this trainwreck moving.
"SHINJI!" Asuka's scream was full of pain, soul-wrenching and horrified.
"You don't have time to worry about him." Rei dropped the words casually, a wave of her hand sending compressed wind towards the Second Child. When Asuka faded into the air, Rei showed no surprise.
"I should know better than to try to fight you at range." She monotoned, bloodshot eyes unnervingly luminescent. "It's where I'm most comfortable, but you're invincible at a distance...so I'll just crush you personally."
Asuka was familiar with anger. She understood the tears welling up in her eyes. Worse than that, though, was the sheer disbelief. Shinji, collapsed on the ground, a quadruple amputee who looked ready to die of blood loss? She'd never been exposed to a situation this...erroneous. How could it have gotten to this?
The molten grief inside of her solidified, almost in an instant. Cold, crystal-clear hatred emerged, and a new creature stood where Asuka had before; Rei had killed Shinji.
Shinji was dead?
He wasn't moving.
Rei had killed Shinji.
She hadn't been able to help him in time.
He'd needed her help, and she'd failed him.
It was her fault he was dead.
Asuka had killed Shinji.
Rei moved forward, seeing her redheaded counterpart breaking down, and prepared to land a killing blow, one arm outstretched to focus a blade of wind.
"For what it's worth, I'm-"
Spikes of water appeared from thin air, pinning Rei in place. A savage, untrained uppercut followed after them, and Rei saw something pathetic and terrifying: Asuka, with hot tears running down her face, collected those tears in midair and began to make a haft out of them. The spearhead formed on one end, but it was curved to one side, almost like a scythe blade. The handle was also too short to consider a spear, which left Rei confused. Racking her brain for an answer, the child of Chaos understood soon enough; Asuka's chosen weapon was a falx, a curving sword designed in ancient times to pierce and rend through reinforced armor and shields like they were made of paper and cheese. Leave it to the pagan princess to come up with that, Rei admonished herself.
Wind ripped the water holding her in place, freeing her to go on the offensive once more. Before she could, however, Asuka's falx came down, cleaving off her right arm before she could register its loss. In the same stroke, the watery blade tore through both of Rei's legs below the knees.
"You're what, you bitch? Sorry? It's too late for that!" The edge of her sword slid through Rei's left arm. "How's it feel to be like this? How is it to be the way you made Shinji?"
Cold silence greeted her, monstrous red eyes looking at her with the kind of compassion and understanding that she'd never been given. What kind of reaction was that? She was angry! She wanted to make Rei hurt! She didn't want that response!
"Answer me, you bitch."
Rei's silence continued, as though she planned to never speak again.
"ANSWER ME!"
"...would you like to know how your father died?"
Again, something so unexpected that Asuka had no counter for it.
"He was the strongest mortal I've ever known. Gendo was more cunning, but Slae'im...that man was a monster. He's the only person who ever learned who I am, on his own. He had the strength of three men, fast as a shark, and he was always training to fight. When he understood what I represented, he began preparing for the day Cernunnos would awaken. To him, it was a father's duty to protect the future that his child would grow up in. He had wanted a son, but I can still remember the tears of joy on his face when he found out you would be a girl." Rei paused, spitting blood.
"He was excited beyond words, which was something of a first for him, in the time that I knew him. He was bloodthirsty, always looking for the next arena to fight in, always trying to find another cause to fight for. When you were born, he knew that he would never need to search again. He was the one who began serious work on the EVA project, and his corpse is what gives Unit-02 its power. My original body rests inside of Unit-01, which is why I couldn't pilot it. But, as for his death...my father ordered it, and Gendo obeyed me when I relayed his command. Shinji killed my father, but the hand that fired three bullets into the back of James' head is still alive."
"Why bother telling me?" Rage and grief were taking over Asuka's mind, the oldest scar she possessed had been reopened with a vengeance.
"You're his only child. The truth didn't need to die with me, and you deserve to know. Now...do what you came to do."
There was no hesitation, a fluid one-handed swing whose low arc swung across. Water cut into flesh, and slit a second smile into Rei's throat. Her flesh seemed to yawn open like a chasm, her head continuing to fall back and rip the cut open further, until the vertebrae in her neck snapped under the strain and her head was severed.
Asuka didn't waste any more time, running to Shinji's side.
"I'm sorry, Shinji...I'm so sorry." Her tears fell, sobs wrenching her body as harsh, ugly crying took over. She didn't register how exhausted she was, or even that she'd just killed someone who was supposed to be her friend. "If I'd been faster, I could've...I could've..." She shoved her face into his chest, crying harder. Crying hard enough that she barely felt the slow thumping in his chest, the shallow rise-and-fall that meant his lungs still worked.
His heart was still beating. He wasn't dead.
She could still save him.
"Ugh..." Shinji opened his eyes, blinking twice. He was looking up at a white ceiling, the one-windowed room looking out on the Geofront. "...hospital. I'm alive?"
He couldn't move his arms or legs. Looking down at himself, he remembered: they'd been blown off.
"Well, that's a problem."
A patch of orange caught his eye, and he looked over to see Asuka sleeping in a chair by the door.
I guess she's the one who brought me here. A little late, but...better late than never.
"Asuka. Asuka, wake up."
"Huh?" She said, stirring and shaking her head. "I'm sleepi-" She nearly jumped when she registered who'd spoken. "Shinji!" She moved to his side, smiling.
"I'd hold your hand, but..." Shinji laughed. "How long as I out for?"
"It's only been a few hours." Asuka said. "Something tells me that we'll be down to just me and Touji to fight in Germany and America, flying out tomorrow."
"Bullshit."
"The hell do you mean-"
"I mean, this is gonna hurt. A lot. Just a warning, I've never done this before."
Clenching his jaw and closing his eyes, Shinji's grunts of exertion gave way to soft gasps of pain. Asuka watched as new flesh came forth on his arms and legs, bones building themselves as muscles layered themselves on top. Blood dripped down to the sheets underneath him, until finally skin grew to keep everything inside.
Chest heaving, Shinji let go of his concentration and rattled off more swears than Asuka had ever heard him say.
"That hurt more than losing them did."
Asuka didn't even say anything, pulling Shinji out of bed and hugging him tightly.
"I was so scared. So goddamn unbelievably scared." She was crying again. "I...I saw you die, Shinji. I killed Rei. I didn't even care that I did that, because you...oh, Odin..."
His arms wrapped around her as though he'd never lost them, holding her close. "It's okay now. Look at me?"
She looked up to him, wondering what he would do next.
"I'll never leave you again." He tilted his head down, kissing her. She was soft and small and cold, wrapped in his larger frame and leeching heat off of his body, and the surprise on her face melted after the immediate shock wore off.
A knock on the door interrupted them, and they separated quickly before it opened; it was Gendo Ikari, and despite his generally unreadable nature, it was clear he was displeased about something. Black, dried blood was cracking off of the left side of his face, from his eye down into his lengthening beard.
"Follow me. There's something I need to show you...both of you."
The pair didn't question him as he wheeled around and walked out, but dropped in behind him and kept pace.
"What the hell is this?" Asuka said in disbelief, looking around the room at back-lit tanks full of motionless bodies. "What the hell is this?"
"This is the dummy plug room. In the event that one of you had been unable to fight, we would have loaded one of these shells into the EVA plug and it would have been able to fight. That, however, is just their secondary purpose."
"They all look like Rei." Shinji noted. "Why?"
"Because they are...not until her consciousness is placed into them, but she is each of them and they are collectively her. Rei, herself, on the other hand? She's not entirely human, though I'm certain you both noticed the signs of that long ago. Her glowing eyes, her skin's deathly pallor. All side-effects of her creation, and the basis on which she was made. I don't know how much the two of you know, but whether you like it or not, it's time for a history lesson. You already know about the one called Kaworu, yes?"
"Yes. Rei called him her brother."
"That's true, and yet not true. According to all the ancient texts that my former colleagues and I had managed to collect and peruse, he is the only survivor of the first attempt at creating life in the universe by the Elder Gods. His 'father' was known by the epithet of the Crawling Chaos, who eventually betrayed the Elder Gods and led to their downfall. In truth, there was a second survivor, the second of that creature's creations. Her name was Lilith, and where Kaworu rebelled, Lilith was the picture of unswerving loyalty."
"Then what happened?"
"Lilith followed the will of her father from beyond the grave, after its death. His spirit was fragmented, buried in her mind, and told her what she was supposed to do. She survived for billions of years, and only died comparatively recently. In fact, she and your father," Gendo motioned to Asuka, "died on the same day."
"Rei said..."
"That I killed him?"
"Yes."
There was silence for a moment before the penultimate commander of NERV let out a long sigh.
"There's no point in denying it, not that I ever have. Lilith used her power to compel me, so that I would be busy and she could do what her father had ordered. He told me who she was, and what she had planned. He...left to go check on you. Your mother was away from home. Afterward, he sat down at the dining room chair and didn't face me. He knew that would make it easier."
"You're telling me you-"
"The compulsion she cast on me was stronger than anything that I've ever heard of Shinji using. there was no possibility I could refuse her order. While I was...indisposed...she oversaw a testing run of Unit-01. Due to interference on her part, the machine went berserk, and she died as she had been ordered to...but I was unable to accept it."
"Father...are you saying that she was my mother?" Shinji had been told how Yui Ikari had died, and how the grave was empty because there hadn't even been a body.
"Yes. Lilith and Yui Ikari were one and the same. When I came to the testing site, I gathered what little remained of her. Most of her had been absorbed into Unit-01, but her blood remained. I synthesized it and began the creation of a synthetic shell that could recreate the person based on the DNA provided. It proved a...middling success. Today is the first time she's ever regained her consciousness and memories from before her death. However, because she wasn't human, I had to supply some of my own genetic material to make the cloning work correctly. To that extent, Rei is both a clone of your mother, and your biological younger sister. Not that she ever knew, or ever will, of course."
"That's ridiculous."
"All the same, it's true. To change the subject: our plan is unmoved. The two of you will fly to NERV Germany tomorrow, and the latest Rei clone will fly to America with Touji...but without any memory of what happened today. Those events are a secret between the two of you and myself, unless you want to reawaken Lilith. Are we clear?"
"Yes, sir."
"Excellent. You may leave."
The lights illuminating the storage tanks went out as the Children left him there, and he stayed long after. Holding the decapitated head in his hands, he didn't need to look in order to know that her eyes were no longer red, and her hair was no longer blue. The darkness was a comfort.
"The ease with which you lie is almost pathetic, my love." He could hear her voice calling out, just in front of him.
"You never loved me." He countered. "Even if you did, your loyalty to your father was greater than whatever feelings you held for me."
"You can lie to yourself, but not to me. I did what I had to so our son could be strong...and you cast him aside because you couldn't bear to remember, while in the same breath turning around to recreate me? Foolish man."
"You're right." While one eye was forced closed by the dried blood, his other eye remained shut voluntarily. The soft smile on his face almost made him seem warm, kind, even friendly; these were not traits that the fearsome Gendo Ikari was known for. "Even now, all these years later, I'm still a very foolish man."
An impossible gust of wind swept through the room, and silence was all that remained after he had disappeared with it.