-1Dark Child: The Return

Episode 1: Assimilation

By: shinjitheassassin

Original Story Concept by: Gunman

Authors Notes: I would like to start off by saying this is only a side fic, an alternate outcome to Gunman's Dark Child series taking place roughly a three years after the third chapter. The events in this fic do not follow the storyline the original author has intended. This is more of an alternate universe. I hope everyone enjoys this as I try to keep it as close to its original concept.

!WARNING!

This story contains a lime/lemon scene, that contains material not suitable for younger readers. Parental guidance is advised. If you are under the age of 18, do not read any further. Remember the ceiling cat is watching YOU!

(Nerv Headquarters)

"Commander Ikari is dead. Both Shinji and Rei are gone. Considering this, I think it's time you all knew the truth." Fuyutsuki said.

"Truth? What truth?" Misato asked, as the word 'truth' caught Kaji's ear.

"The truth about the Angels, and why NERV really exists." Ritsuko stated.

"That would not be a good idea." a familiar voice stated. Catching the attention of everyone in the room to look to the door where the newcomer was. Stepping into the little light the room had to offer, everyone gasped in surprise. Though they had just seen him killed, Gendo stood in the door way.

Just like the bastard to clone himself Ritsuko thought to herself.

"C-c-commander?! But I thought….."Maya stammered, dumbstruck by the sudden appearance of the one they had just seen killed moments ago. "But how?"

"That is irrelevant." The commander stated walking over where his previous self was and removed a small item from the pocket which had just barely missed from being cut. Turning his attention to his second in command. "Report on what has just happened in five minutes" he said and turned, walking out. "And clean up that mess."

"That was…. Weird." Asuka said as she stared on, her eyes darting back and forth between the mess that once was the commander, then to the commander who had walked out the door. The rest just remained there speechless. It took minutes for everyone to regain their composure, a Nerv detail crew had already reported to remove what was left of the former commander, carting him out in eight body bags. Fuyutsuki had left to go report the matter to the new commander.

(Commanders Office…I guess you would call it)

"I said in five minutes." Gendo cut to the chase, his second in command was nearly a minute late.

"I apologize, I was getting the video feed that had recorded the incident." the elderly man stated as he handed the commander a disc. "I figured it would be easier then trying to explain it with words."

"Indeed." the commander stated, and placed the disc he had just received into the terminal on his desk. Viewing the event. Though he couldn't be seen behind his gloved hands that once again sat bridged before his mouth, he made a frown in disgust. "Where are they now?"

"We don't know sir, they seemed to have just disappeared."

"I see." the commander replied. "Order all security personal to shoot the third child on sight, I will not have this incident repeated. Also, continue the search for the First Child."

"Yes sir." the elderly man answered, and left to do so.

However many thoughts bothered Gendo, though his face did not betray it. This is going to prove a problem in our project, I cant simply revive a new Rei without the others becoming more curious then they already need to be. He then took out the small item he had taken from his former self and reset it. It was a heart sensor, so that if the persons heart stopped beating, a new Gendo would awake, however there was no need for it anymore, he was the last one.

(Above Ordo 7)

Blaster fire surrounded The Infiltrator as Shinji maneuvered it to avoid the firestorm that besieged them. Rei was in the co-pilot seat focusing on keeping their rear deflector shields up as another barrage hit them. They had failed to assassinate Sidious and were forced to flee; their allies dead. Shinji had moved to soon to claim revenge for his former master and with his confidence in his power and team he had foolishly under estimated the Sith Lord. The Infiltrator was a fast and maneuverable ship, capable of out running most of the fleet easily, but the ship that now pursued them was The Chikara, a prototype battle cruiser. Despite its large bulk it was able to keep up with them. It had the appearance of an over sized blimp, Shinji couldn't help think. (A/N: Think Protoss Carrier from Starcraft would best fit the description) It released another squadron of TIE fighters to attack the Naboo ship. Then the large blimp did something that surprised Shinji, stopping its pursuit, the ship then began to split into quarters, long ways down its haul.

"MASSIVE ENERGY READING EMITTING FROM THE SHIP!" Rei exclaimed.

A green glow came from the parted ship as it continued to build up energy to fire its primary, and secret weapon. This weapon was the prototype of what would later be on the Death Star.

"Its locked on to us" she continued, a hint of worry in her voice.

"Do not worry, such a beam no doubt will take time to recharge." Shinji calmly said as he used the Force to navigate his way through the laser blasts that continued to fall upon them from the TIE fighters. "I have an idea."

"If that things hits us, its over."

"This is true, however a weapon of that energy will require a large amount of power and will no doubt keep it from moving forward when its fired, if it misses it will give us the time we need to make our escape" Shinji explained.

"I trust you." Rei replied. Time seemed to have stood still as she looked over at the man in the pilot seat, in the time she had stood by his side, so much has changed. With their training, and missions. Those who had once known the two would hardly recognize them now. She then couldn't help but wonder how their former comrades would see them now. She was soon shaken out of her thoughts as a bright green light shot passed them as Shinji just barely maneuvered the ship, his timing just right. The beam passed The Infiltrator and hit the planet below them, just happening to hit exactly where the temple was that originally took Shinji back to his home. The next series of even happened in the blink of an eye. Within seconds after the beam hit the planet, the planet began to crack, a jade green light pushing through the cracks as the planet began to break apart. Then it erupted into a massive explosion, the jade light flowing out, engulfing both ships before retracting back into itself, pulling both The Infiltrator and The Chikara with it, disappearing; one of the TIE fights managed to get one last shot off, hitting The Infiltrator, disabling their main power drive before being crushed by the force of the explosion.

(Earth; Our Dimension)

"Report on the progress of your search for the First Child." Gendo stated, looking at his second in command.

"Nothing yet sir." the elderly man answered.

"I see, she must be found." the commander said. 'Our future depends on it'

It had been two weeks since Rei had disappeared from the command center. Most of the staff was on edge, especially those who were present during the incident, though no one wanted to talk about it. Misato was on the verge of a mental break down at the loss of Shinji, the apartment had quickly fallen apart. Asuka on the other hand had been glowing with praise, as she was the only remaining Eva pilot, pushing her stock through the roof. However there was a problem in this, since the disappearance of Rei, the Angels had ceased their attacks, proving frustrating to the Second Child. Though no one could tell why, but assumed it was only a matter of time before they would attack again. Ritsuko had locked herself in her office most of the time, doing who knows what.

Meanwhile, above the earth a brilliant green light flashed, spitting out The Infiltrator, spinning it wildly as the occupants struggled to regain control as the ship plummeted towards the planet. Using its many thrusters to straighten out the ships course.

"Fire the emergency booster engines!" Shinji ordered. Rei did so, the ship began leveling out allowing them to regain control.

"Secondary power at fifty percent, we're going to need to land for repairs." Rei stated as she over looked her console, alarms sounding throughout the ship. It was then that Shinji noticed the planet they were heading to, though they still couldn't see anything that would serve as a marker to where they were, there was a strange sense of familiarity to it. It then occurred to Shinji where they were, a smile crept across his face.

"Rei?"

"Yes Master?"

"Does anything look familiar?" he asked

Rei took a moment to observe out the window in front of her, she couldn't recall anything. Then it hit her, this was….home. She smiled, soon her previous thoughts would become a reality, what would her former comrades think of her now. Shinji continued to pilot, choosing to land the silver ship a few miles outside of Tokyo-3 in the dense forest, this would offer natural cover for them to go unnoticed. He wanted to land as quickly as possible, not know when or if their pursuers would attack again. Setting down in an ideal spot, surrounded by trees large enough to conceal the silver ship. Shinji swiveled his chair around, punching random buttons on the monitors, running a complete systems check to get the full report on everything that was damaged. They were lucky, the damage was minimal, something they could fix easily.

"Small breach in the power core, and minimal system damage to the shields."

"Can we fix it?"

"Yes, we have enough supplies on board to do so." he replied. "It will take some time though."

"I understand." Rei said and left the cabin, setting off to begin the repairs. During her adventures with her husband she had learned the mechanics of the ship rather well, mostly due to trial and error, though he had been there to guide her. Shinji had followed after her. The two spent nearly half the day doing repairs, and making little headway as complications ensued, or rather distractions as they worked close together. In the fading light, they decided to set up camp. Digging into their survival units for their meals. Seeing the weather was nice they decided to eat outside, starting a small camp fire. Despite all the technology they had, years beyond anything currently on earth, this seemed more comfortable. Silence hung over the two as they ate, until Shinji spoke up.

"I feel I must apologize." he began, remnants of his former self partly showing.

"What for?" Rei asked, confused.

"I forced you to come with me, when I came back." he explained. "I drugged you to make you mine."

Rei smiled. "Mind tricks only work on the weak minded." she simply replied.

"What do you mean?"

"I would have come for the asking." she revealed. Though the pill had done its job, she allowed herself to fall under his influence that day. The truth was, she wanted to go with him, she wanted to be rescued from that life; she wanted to be desired and needed. Shinji smiled as he looked at her.

"Rei-chan?"

"Yes?"

"Do you love me?"

"Yes Shinji-kun."

"Will you promise to serve me, as my lover and partner? As my bride?" he asked, moving closer to her, staring into her crimson eyes as he spoke these words.

"Yes, my lord." she smiled, pulling him closer to her as she answered. Their lips meeting passionately. Laying back she pulled him on top of her, continuing to kiss each other. Shinji then broke the kiss.

"Then I take you as my bride, Rei Ayanami. You will love me and no other. You will desire no other but me."

"Yes, my love."

"You are mine forever, Rei-chan. Because I want to love no one else." he said as he looked into her crimson eyes as he embraced her for another kiss, which she returned with the same force and passion. The pledge reset and cast in stone.

He brought his right hand, placing it at the small of her back to support her as she grasped the back of his neck, keeping him close to her as they continued to kiss, heat building between the two. Slowly they began to strip each other of their Sith garments. Exposing her breasts, he began to kiss down her neck, slowly, teasing her as he went, gasps escaping her lips as he proceeded. Reaching her firm breasts, he took one in his mouth, gently sucking on its nipple, while his hand cupped the other, pinching its nipple between his finger and his thumb. Electricity was coursing through her body as waves of pleasure washed over her again and again. As his mouth continued to keep one of her breast occupied, he finished removing the rest of her lower clothing, leaving her completely exposed to him. Stopping for a moment he looked up at her, her eyes were closed. Smiling he leaned down again, kissing her deeply on the lips before leaving a trail of kisses and soft bites down her body, licking the valley between her breasts and continued kissing along her sensitive stomach. He then reached her lower regions, She let out a surprised gasp as he probed her entrance with his tongue, spreading her lips apart with his fingers, he continued to work her vessel, probing his tongue in and out, and flickering it along her clit. Moans followed forth from her lips, arching her back, she cried out as she came, unable to control it any longer. That finished, Shinji smiled and began working his way back up her body, reaching her lips again. Pressing his lips against her, they began another passionate kiss, their tongues snaking around each other. She spread her legs more, to offer him entrance. His hardened member rubbing against her entrance, causing her to gasp in anticipation. Slowly he pushed himself in, slowly working his way until he was at the hilt. Settling there for a moment, he began to thrust himself in and out. Deeply kissing her as moans escaped both of them, moans of pleasure, unbridled pleasure. They continued for hours, altering positions as they went. Not stopping until well into the late evening, before Shinji finally came, releasing his essence and planting it deep within her body. Finally the two succumbed to sleep, pulling the sleeping bag up around them, snuggling close together, giving one another one last kiss good night.

(NERV, earlier that day)

Typing could be heard throughout the dark corridor to anyone who would chance to be down in the lower depths of Central Dogma. The light from the small computers monitor reflecting off the unshaved mans eyes.

"So. that's what it is." he spoke softly to himself. Since the sudden return of the commander he had become curious to the events. He had seen the commander killed, only to have a new one appear. After two weeks of hacking and digging he had finally uncovered the truth behind it. "Seems he's not a very popular guy." he smirked. There was a sudden crash just down the corridor, quickly he shut off the computers monitor and pulled out his side arm, sitting silently waiting to see what it was. He then felt something press against the back of his head.

"Find what your looking for?" a familiar voice said.

Lowering his gun he replied. "Feeling better?"

"Yes, thank you for your concern." Misato said, a hint of venom in her voice. "Now why are you down here?"

"Well you see, I was curious." he began, in his usual swagger.

"Of what?"

"Our commander, we saw him sliced into eight pieces, thrown against the wall; and yet he is alive."

"So he had a body double, not uncommon."

"Yes that was what I first thought too, but I was satisfied with just that. So I did a little digging, and guess what I found." he smiled as he reopened his lap top revealing medical documents for Ikari, Gendo. Misato looked in shock.

"Complete genetic replication, he was a…..clone?"

"Is a clone, turns out the original Gendo Ikari died shortly after second impact, these copies have been continuing his work."

Misato was at a loss for words as this was revealed to her. But then again, it slowly crept into her mind that it made sense, he was always detached from everyone else. Lowering her gun from his head, securing it back in her holster.

"Also, I pulled up the video feed from the other day."

"What video?" she was still confused at first but it came back to her. "Oh, did you find anything new?"

"Well not really, but I found an answer to every ones questions."

"Was it Shinji?"

Kaji quickly punched a few of the keys, opening a new file on the computer. Playing the video in questions, then slowing it down very slowly as the camera that was in the room zoomed in for a close up shot as the man looked at the blue haired pilot. "Here you can see his expression soften, a very familiar face."

"IT IS SHINJI!" Misato exclaimed, then quickly slapping her hand over her mouth, remembering where they were. "But how did he change? And get so big?"

"That I can not answer, the only thing I know is that it was him. I am also curious as to how he returned and why he only took the First Child with him."

The two froze as they heard another pair of footsteps down the main corridor. Kaji quickly shut his monitor and pressed himself and Misato against the wall to reduce the chances of being seen. Two figures passed, one of a woman, the other a man.

"Are you sure about this sir?" the woman asked.

"There is no other way, we need the first child to proceed." he replied as the two entered a large room surrounded by an aquarium like tank. The woman walked over to an instrument panel and read the results, satisfied she turned to the man.

"When do we begin?"

"We will begin in two days, giving the third time to heal." the man replied.

"Wont the sudden appearance of the first child bring about unneeded attention from the others?"

"No need to worry, we will simply report that we had located her."

"I see."

"Let us go, we have much to do."

"Yes sir."

With that the pair left, not once noticing that they have been overheard. The foot steps faded away, as a mechanical hum signaled that they had entered the elevator.

"And so another piece of the puzzle falls in our laps." Kaji smiled.

(The Infiltrator)

Morning found the two Sith cuddled close together, their fire had gone out sometime in the early morning hours. Shinji slowly stirred awake, smiling as he saw the azure haired girl laying in front of him, her crimson eyes looking up into his.

"Morning Rei-chan" he smiled, kissing her forehead gently.

"Morning Shinji-kun" she beamed. The two of them got up from where they laid and proceeded to secure their attire. Donning their usual all black clothing. Shinji thought for a moment as he looked at Rei. She noticed and smile.

"What are you thinking about?"

"I feel I need to give you a proper name" he replied.

"Proper name?"

"A Sith name" he paused for a moment, then smiled. "Rei Ayanami, from this day forth, you shall be known as Darth……Shi"

"Shi? Death." Rei stated.

"Yes, fitting for one who accompanies a demon."

This brought a smile to the blue haired woman, kneeling down before him she bowed her head. "Thank you, my master"

"Arise, Darth Shi, I have an assignment for you."

"What is it, my master?"

Shinji smirked. "I want you to return to Nerv, and negotiate its complete surrender to me by any means necessary." he stated, though it had seemed like a lifetime ago, he recalled the military organization he once served by force. Returning now, he saw the advantages he would have having such a group under his command.

"It will be done my lord"

"Go now, I will arrive there within a day, after I complete the final repairs" he said. With that, Rei secured her own light saber to her belt and set off in the direction of the city, wrapping her black cloak about her, placing its hood over her head. Taking one last look behind her, she didn't want to leave him, but he had given her a mission to do on her own, and she would not fail him. Turning, she left, leaving the wooded area. Tokyo 3 was no more then two miles away, a distance she covered easily as she walked on, gaining curious stares from some of the people along the streets as she made her way through its down town area. She didn't pay no mind to them as she continued on her way. After two hours of walking, she reached her destination, standing in front of a line of doors that led into the Nerv base. Looking down she saw the card slot for employees and others to slide their card through to gain entrance. She frowned some at this, she had lost her ID card years ago, her frown then became a grin, raising her hand she moved it sideways, causing the doors to open as she extended out with the Force. She then entered, she was immediately stopped by two guards. Rei smirked as she looked at the two guards, brining up one hand she extended two fingers towards the first, for some reason causing him to convulse against the wall, then turned to the second, doing the same. She then moved on leaving both guards to die as they gasped their final breathes. Continuing on she rounded her second corridor, she had been in the building enough times before to know where she was going. She was then stopped when someone called her name.

"Rei?" a female voice asked from behind her. Before she had time to answer the woman behind her hugged her, almost tackling her. "REI IT IS YOU!" Misato exclaimed. Rei did not take kindly to this physical action, but gathered nearly every ounce of will power in her body not to cut the purple haired womans head off. "Commander Ikari is going to be pleased to see you were able to escape!"

Rei did not comment at first, turning around to face the major behind her. "I must speak with commander Ikari at once, its very urgent I do so." She repeated

"Of course, I will let him know right away, in the meantime lets get you changed into something more comfortable."

"These are fine, please the commander." Rei was becoming impatient to say the least, and it was starting to sound in her voice. Misato nodded in acceptance andled Rei down the series of corridors that made up the Nerv complex. They soon arrived at two large black doors. Two more guards where posted there. Due to the incident Ikari had stepped the security up, everyone had to be searched before entering his office. While one guard stood ready at the door, gun in hand, the other proceeded to remove Misatos gun, the moved to Rei, patting her down, finding her light saber; though he didn't know what it was. Again Rei didn't like it but held back as the guard led the two into the room where Gendo sat behind his desk, his hands folded across his mouth. The guard set the two weapons on the desk before him and quickly turned to leave, not saying a word.

"What is it Major?" Ikari asked as he looked over the two, his eyes focusing on Rei for a moment.

"Sir, Rei Ayanami has returned."

"Where is she?"

Misato said nothing at first as she gestured to the eighteen year old woman beside her. "This is Rei Ayanami."

"I see" the commander answered as he studied the girl in front of him. Noting the eerie resemblance of the clothing to that of his former selfs attacker.

"Sir;" Rei began, "I request that Dr. Akagi and the remaining Eva pilot accompany us here to hear what I am about to say, for it surely will affect them as well as the rest of Nerv." the names coming to her mind as she continued.

Gendo frowned at this but nodded, pressing the intercom button on his desk. "Bring Dr. Akagi and the Second Child to my office." he said, canceling the communication before he got an answer.

"Can I get you anything to drink Rei?" Misato asked, becoming more cheerful like her usual self.

Rei frowned for a second, they wouldn't have any of the drinks she enjoyed at the cantinas, she then looked at Misato.

"Tea would be fine" she answered, it was all the really had to offer. Misato nodded and left. Returning a few minutes later with a paper cup from the vending machine in the break room. Rei accepted it, but offered no thanks. Soon the other two arrived.

"WONDER GIRL!" Asuka cried out when she saw the blue haired woman. If looks could kill, Asuka would have been dead from the glare she had received from Rei, causing the red head to flinch under her eyes. She had always hated being called that, and if she wasn't careful, Asuka would be called 'Dead Girl' Rei thought to herself.

"You said you had information pertaining to the future of Nerv, what is it?" Ikari stated from his chair, getting straight to the topic at hand.

"Of course" Rei looked to him, a slight smile flashed on her face. "I have vital information about the attacker." she began.

"And that is?"

"He is planning an attack on this base." she simply stated. "He will assume control of it" she continued , her tone of voice absolute.

The commander frowned again. "And how does one man take over an entire base? It is of no concern, he wont make it passed the front gates." Ikari counted, fully confident in his security. "But I am curious Rei, tell us your story, what happened after he kidnapped you?"

Rei smiled again as memories flashed in her mind, but the smile was brief as she looked over the commander. "Very well, I will tell my story to you." She then proceeded to recount the events that took place after her 'abduction'. She left out their marriage, not wanting to draw any suspicion to herself and about how he had taken her on as his apprentice, this was more to explain the clothing she was wearing, having seen the worried look upon the commanders face. When she had finished she took another drink of her tea, which had cooled off.

"I see."

"But how did you escape from him?" Misato asked. This time Rei smiled, large enough for everyone to see. This no doubt brought about fear in them.

"Escape? Who said I escaped." Rei grinned.

"But you…."

"I said nothing of the sort, you assumed" Rei pointed out. During this time Gendo had paged the two guards to enter the room. Rei smirked again. This is going to be fun she thought as she glanced behind her. "Don't trust me Commander?" she asked, mocking the innocence in her voice.

"There is nothing you can do Rei, with your weapon right here." Gendo stated as he patted the light saber next to him on the desk. He had reviewed the video enough to know that what it was, though he didn't know its name.

Rei smiled again "I no longer go by the name Rei Ayanami." she stated. "My name is Darth Shi." a hint of hatred and anger in her voice. At this the two guards behind her raised the guns, aiming at her back, ready to open fire. The next few actions happened fast. Without so much as a warning Rei reached out her right hand towards the desk, stretching out with the Force and grabbing her light saber, brining it to her hand as she jumped up. Igniting it as she spun around in the air, she landed behind the guards before they had a chance to turn around, she slashed across them, cutting them in half at their waist. She then turned around, facing the door and threw out her left hand, slamming the doors shut before the others could escape. Grinning she turned to face the horrified Commander. Extinguishing her saber she raised her left hand and made a movement of pinching something in mid air between her two fingers and thumb. As she did this, Ikaris hands came up to his throat as he tried to breath, something was choking him.

"Now that I have your attention Commander, I will give you one chance that might save your life. Surrender all of Nerv to my Master." she stated coldly.

Master? Asuka thought to herself as she stared on in horror. Even greater fear gripped her when she realized she might be next due to the fact that constantly in the passed she had always bullied Rei

"I…..I-I ca-n't" Ikari struggled to speak. At this Rei released him from her grip and sighed.

"I see, well I supposed we will do things the easy way." she smirked again, leaping forward landing on top of the desk, igniting her saber again, swung at a slant. For a few seconds Gendo sat their, a shocked look at his face. Then a line began to form running from the top right of his head towards his left cheek, as the top part slid down, landing on the floor, leaving the body remaining in the seat with half a head.

"Its finished, all of Nerv is under my command until my Master gets here." Rei stated as she extinguished her saber, securing it back on her belt. Pushing the body out of the seat she sat down in it, not even second glancing the corpse.

"He's….. he's coming here?" Asuka asked in fear.

"Yes, he will arrive shortly, and I warn you, he is not as forgiving as I am." she warned. "Have someone clean up this mess." with that she dismissed the remaining three in front of her. She then turned her attention to the elderly man who lay on the floor just behind her, gasping for breath. The events that had transpired had triggered a severe heart attack. Smirking some she looked around the dark room, the sepheroth tree painted on the ceiling above her. Within hours a report came to her desk stating that an unidentified object was approaching their location. With that news she ordered all personal to the inner landing pad just inside the Geofront. The soilders standing at attention as the silver ship descended, two separate groups of them, creating a path down the center where the ship landed, lowering its boarding ramp. Rei approached the entrance and kneeled down, bowing her head as another cloaked figure descended the ramp.

"Arise Darth Shi." the man said. She did so

"It is done my lord."

"Good, very good. Everything is going according to plan" he smiled as he turned to look at her while the walked.

"Yes, the beginning of your own empire" Rei coolly remarked with a grin.

"Our empire." he corrected her. "Every emperor needs and empress." he smiled.

To Be Continued…..

Authors Notes: Well there it is, Part 1 of the Dark Child side fic series, At this time I am not sure how many parts there will be. I would like to thank Gunman for giving me permission to do this side fic, and hope that I have stayed true to its original concept. As stated previously this is an alternate universe fic as to what would happen if Shinji and Rei returned and took over Nerv and so on. There are some references to the original Star Wars movies, like Rei force choking Gendo. I hope everyone enjoyed reading it as much as I did writing it. Also there are a few other Japanese words in this:

Chikara Power

Shi Death

Oni Demon

For those who are curious, Reis light saber is much like Darth Mauls, except it can be split into two separate sabers.

Pre-Readers

Gunman

My room mate, always hanging over my shoulder

Special Thank to Gunman for allowing me to run with this.

Disclaimer: I do not own Evangelion or any of the Star Wars characters, those are property of their respected owners. Evangelion belonging to Gainax and its respected affiliates and Star Wars to George Lucus.