Saint Shinji (Draft)

Evangelion crossover with Saint Seiya

(This takes place shortly after the 13th Angel)

Chapter 2

Rei woke within her dark and empty room, something disturbed her from her sleep, a feeling of displacement. This feeling is alien, yet familiar to her, it troubled her because normally she did not have feelings such as this. The only time she recalled having feelings similar was when she found out that the Third Child had vanished or left, the Commander would not tell her which and she had been unable to find out for herself.

She breathes, "Ikari-kun…"

She wonders why she would think of him now, when in four years she had only briefly thought of him. She didn't know it then but now she realised she had missed him, since he was the only one that had ever talked with her as a human and a friend. The phone rang, shaking her from her thoughts, it was Dr. Akagi calling her in for tests. She sighed and got dressed, preparing to make her way to NERV.

Asuka was again, ranting about something as she changed into her plugsuit. She grumbled, "Stupid tests! Why do we need to do them anyway, its not like the Angels attack anymore"

She hurriedly put on the plastic suit, and pressed the button on her left wrist, as usual the suit automatically sealed itself and moulded to Asuka's now mature body.

She muttered, "Right! Let's go Asuka!"

Sitting in the test plug, Asuka shook her head to dispel the aching of her head, it was strange, and she couldn't seem to focus today. Plus it was her period, she was getting aggravated, even more than usual. For some unknown reason, her mind kept on drifting until it homed in on one memory. Shinji. She thought to herself Why the hell am I thinking about that baka?

Ritsuko's voice cut in over the intercom, "Asuka, pay attention! Your sync ratio is dropping"

Asuka's irritated reply was, "Yes, ma'am!"

Misato asked, "What happened?"

Ritsuko glanced over the read-outs, "Nothing much it seems, Asuka's sync ratio dropped momentarily but it's okay now"

Misato frowned, sometimes her old friend sounded so cold and logical that it pissed her off but she let it pass since it was her way, at least at work. At college, Ritsuko was a bit different, despite her workaholic habits. She was about to say something else, when without warning, the warning klaxons went off.

Misato yelled disbelievingly, "An attack? Now?!"

Ritsuko spoke into a microphone, "Commence activation procedures for Units 00 and 02. Transfer pilots from test plugs to entry plugs"

Both of them ran to the elevator, which would take them to Central Dogma.

Misato shouted at the three technicians, "Status report!"

Hyuuga yelled back, while trying to process any useful information, "It just appeared out of nowhere, recon satellites two and six have been knocked out"

Ritsuko: "What the hell is it?"

Aoba: "We don't know. Putting it onto main screen now!"

The big screen flashed and all they saw was a round ball of light before the screen fizzed out when the satellite was destroyed.

Misato: "Is it producing a blue pattern?"

Maya panicky: "We don't know, its moving too fast"

The screen flashed again this time showing a different view, in the mountains surrounding Tokyo-3 and a streak of light falling towards them.

Hyuuga: "ETA five minutes. Point of impact should be three kilometres from us"

Misato yells out her orders: "Evacuate all civilians and put Evas 00 and 02 on standby. As soon as that thing lands, scan it and send out teams to investigate"

Ritsuko squints at the image on the screen, "It's too small to be a meteorite or a comet" Quickly, she plotted out some trigonometry calculations in her head, 'It's angle, it's too controlled and shallow to be a normal meteorite'

She calls out to Maya, "Maya, what are the Magi's prediction?"

Maya still entering information on the anomaly, "It's fifty: fifty odds"

There was a brief flash of light when the object collided with a mountainside.

Aoba: "Seismographs only picked up a small tremor, almost too small for an object travelling at that velocity"

Misato: "That's it, launch the Evas. Unit 02 will take point and Unit 00 will be backup, understood?"

Asuka and Rei's voice came through the intercom, "Yes ma'am"

At that moment Gendo and Fuyutsuki chose to walk out onto their commander's platform.

Gendo settling into his usual position, "Update"

Ritsuko: "Sir! There's been an unidentified object that came from orbit eight minutes ago and has landed outside of Tokyo-3. The scans hint that it is not a normal meteorite"

Misato: "Teams have been sent to investigate and the Evas are mobilised ready for any threat"

Gendo nodded to Misato, "That is satisfactory. Update me on any new occurrences"

Aoba, rapidly tapping buttons on his console, "Satellite zooming in on point of impact now!"

One half of the screen showed where the object landed, as expected there was a crater but one difference was that this crater had a small hole in it.

Misato: "What's that hole?"

Suddenly another alarm went off, and this time it was Hyuuga who panicked, "Geofront's been breached"

Misato screams, "What was that?" She turned to the intercom, "Asuka, Rei get back into Geofront now! Use port seven"

Asuka, "What the?! OK, I'm coming"

 Units 00 and 02 descended into the Geofront, cautiously they advanced on the breach. Unit 02 holding a spear, stalked forward while Unit 00 holding a pallet rifle, backed her up.

Misato: "Ok. AT fields full power. Be ready for anything"

Asuka: "Understood, Misato"

Rei stayed silent, keeping an eye out for anything. After awhile, she spoke, "I'm not detecting anything. My sensors are normal"

Asuka: "Neither am I. There's nothing here except this hole"

Ritsuko shakes her head; "The Magi are withholding judgement"

Misato crosses her arms, "What does this mean? Fine, you two get back to base but be ready for action at any minute. Change alert status to yellow until we find out what the hell happened"

Gendo stands up, getting ready to leave, "I'll leave this in your capable hands, Major Katsuragi. Report any findings to me"

That was when a voice reached their ears, "Leaving so soon, Father"

Everybody in the Command Centre freezes, Gendo spun around very surprised to hear the voice again, true, it was deeper than before but it was very recognisable as Shinji's.

Misato's eyes glimmered as she looked around frantically, "Shinji? Where are you?"

Shinji's voice held a trace of amusement; "I'm right here"

From a previously shadowed corner step out a man, Gendo, Fuyutsuki, Ritsuko and the three techs look at this new person in surprise but Misato didn't show any hesitation. Immediately she ran to him and hugged him fiercely, she cries into the man's chest, "Shinji! You're alive. It's you, it's really you"

The man's arms came up and wrapped themselves around Misato, his eyes shimmering as well, he spoke hoarsely, "Yes, Misato. I'm alive and I'm back"

Ritsuko walks up slowly, "Shinji?"

Shinji looks up, "Yes, Ritsuko"

Ritsuko almost didn't recognise his face, it was different from the Shinji she knew it had matured, developing an angular characteristic like Gendo's, she finally spotted the difference, it was tanned and a bit weather-beaten but it was Shinji's. Laughing she rushed over and hugged him as well, adding her own tears of joy, for a friend returned, alive and well. Soon the other three techs joined the other trio, welcoming back a friend, with hugs and handshakes. Gendo and Fuyutsuki stood shock-still at Shinji's return, Gendo stared at his son and once again turned to walk away.

Shinji looked up and frowned at his father's retreating back. His gaze shifted to Commander Fuyutsuki, who met his gaze and smiled at him, Shinji acknowledged the smile with a nod of his head.

Shinji turned back to his friends, managing to stop Misato crying but not getting her to let go of him.

Shinji said, "I like to see Asuka and Rei. How have they been?"

Ritsuko replied, "They're fine. We just sent them out in their Evas"

Misato gasped, "Oh my god! We forgot about the breach"

The three techs jump in alarm, but Shinji silenced them.

Shinji: "It's okay, it was something I used to get into here as soon as possible"

The group of adults stared at him wide-eyed, Shinji turned to go, "Let's go. It's been awhile and I want to see everyone I missed"

The mystified group followed Shinji to the Eva cages.

In the briefing room, Asuka and Rei was sitting around impatiently, well at least Asuka was. She was pacing around the room; occasionally glaring at the door while Rei sat on one of the chairs passively. Finally Asuka snapped (No, she hasn't gone crazy, even though that would explain a lot of things), "Where's Misato? What's taking her so long?"

The door opened and Misato stepped in smiling, all traces of tears wiped away.

Asuka growled out, "What's up? Why are you so happy?"

Misato choked, "It's nothing except…"

Asuka looked at her guardian sceptically, "Except what?"

A deep voice interrupted them, "Except that she's overwhelmed with joy"

Rei looked up, breath catching in her throat, as Asuka's eyes narrowed dangerously, "Misato, what's going on here?"

A figure taller than Misato stepped through the door, "Well, apparently me"

Rei squinted at the shadowed figure, "Ikari?"

The figure stepped forward, "Yes Rei. It's me"

Asuka took one look and fainted.

Asuka woke up later to see a familiar, yet unfamiliar face looking down at her.

Asuka closed her eyes and moaned, "What happened?"

The same deep voice she heard before spoke, "Well, it seems that you fainted"

Asuka still with arm over her eyes snorted, "Nonsense, I don't faint. I never did and never will"

Deep voice seemed uncertain, "Well, okay"

Suddenly Asuka realised something, with a scream, "Get away from me, pervert!!" She launched herself upwards and away from the strange person. Asuka stood, half-crouched in a guard position, glaring at the stranger as he stood. He was tall, slightly taller than she was; his dark hair was long, unkempt as if he just emerged from the wilderness, it settled wildly on his shoulders. His body was fit, lean and hard from exercise and rough living but wasn't that heavily muscled. His clothes was different as well, he wore a blue sleeveless shirt that outlined his torso, black trousers covered by fur at the shins, his arms were wrapped at the biceps, and from forearm to wrist to hands similar to a boxer.

Asuka demanded, "Who the hell are you?"

The stranger looked confused, and if she read right, a little disappointed, "Don't you recognise me, Asuka?"

Asuka started to shake her head, then stopped as that tone snagged a memory, she looked closer, then, "Shinji? Is that you?"

The stranger, no, Shinji nodded, "Yes, it's me. In the flesh"

Asuka looked about to break down, Shinji immediately rushed over to help, only to be rudely disabused of his assumption as Asuka's fist made contact with his gut, it was only luck that it wasn't lower. Shinji doubled over, gasping for breath, while Asuka straightened, rubbing her knuckles, she thought 'Damn! That hurt, what did he do to his gut?"

The door opened and Rei stepped in with damp cloth in hand, followed by Misato. Both looked at the figure keeling over, Misato sighed, "You two haven't seen each other for four years and the first thing you do is FIGHT!"

Asuka protested, "It wasn't my fault! Pervert boy here, tried to grope me"

Shinji made his own protest, "No I wasn't. I thought you were about to faint away and tried to catch you"

Asuka shook a fist at him, "Are you saying that I'm weak?"

Shinji hurriedly backed away, shaking his head, "No, definitely not. Didn't cross my mind for a sec"

Asuka crossed her arms and huffed, "Good!" Surprising everybody, she then walked over and hugged him, "That's because I missed having you around. Do you know what's it like having Misato cook for four years?"

Misato: "Hey!"

Asuka grinned; even Rei had a small smile, having tasted Misato's cooking once, Shinji's mouth twitched. Then with indiscriminate force, Asuka slapped him, the others looked shocked, "And that's for disappearing without a word"

Shinji turned his head to face Asuka, "Nice one, but to be more effective, put your shoulder behind it"

Then Asuka did exactly that, Shinji staggered. Coolly he worked his jaw before he answered "As for disappearing I didn't have a say in that but I did chose to stay away until now"

Misato spoke up, curiosity aroused, "And why did you stay away?"

Shinji looked around, "I think we need a bigger audience and Father would need to hear this"

Soon the people Shinji deemed necessary to hear what he had to say was present, with the exception of his father and Commander Fuyutsuki.

Shinji sighed, "Well I knew he would be a no-show but while we wait for him, I would like to make amends"

Misato looked at him puzzled, "Amends?"

Shinji looked downcast, "Yes, amends. Misato, do you know where Touji is right now?"

Misato and Asuka sucked in their breath, it whistled when they breathed out through their teeth.

Misato: "Touji's fine. He's on base at the moment"

Shinji looked startled, "Why?"

Misato looked uncomfortable so Ritsuko spoke for her, "Touji's still designated as the Fourth Child and due to the little stunt you pulled today he's been called in for duty"

Shinji was stunned, "How come he wasn't out with the others?"

Ritsuko took a deep breath, "Well, since the Angels stopped attacking, NERV's been working on a reduced budget and with a couple branches disbanded, we haven't had the resources to build another Eva, but we've been putting what's available into rebuilding Unit 03 after we deemed we salvaged to be uncontaminated"

Shinji flinched when Unit 03 was mentioned but aside from that he was impassive, "Fine but how could he pilot? When I last saw him, he was missing an arm and a leg"

A person called in from the door; "It's fine now"

Shinji spun around, "Touji?"

Touji ran forward and grabbed his friend in an enormous bear hug; Shinji after a few shocked moments returned the embrace.

After the two separated, Touji clapped Shinji on the shoulder, both males of equal height now, Touji laughed happily, "It's nice to see you, Ikari!"

Shinji slowly smiled, "I suppose it is, Touji" Then he noticed Touji's limbs, all four of them, he exclaimed, "How did you get…"

Touji put in for him when he was unable to continue, "My arm and leg back, they offered to give them back to me if I stayed with NERV"

Shinji: "That still doesn't explain how you got them back"

Ritsuko spoke up, "We cloned them and regenerated any damaged tissue, it was a process similar to repairing an Eva"

Shinji was thunderstruck, "That's…that's amazing"

Touji swinging his restored left arm, "It took awhile but it was worth it. I can walk, run and play basketball again"

Then a cold voice cut through them, "So what have you got to say, pilot?"

The people present (Asuka, Rei, Misato, Ritsuko, Maya, Hyuuga, Aoba, Touji and Kaji) flinched with the exception of Shinji. They all turned to meet the Commander, Shinji said dryly, "Why Father? So nice of you to join us"

Gendo ignored his son's sarcastic remark and stepped into the room, coldly he asked again, "What have you got to say that is so important?"

Shinji nodded, "Why don't we all sit down, it would help"

Gendo shrugged and seated himself on a nearby chair, accompanied by Fuyutsuki. As soon as everybody was seated, Shinji, who stayed standing, began to talk, "Well, first of all I have to say it's kinda nice to be back. And secondly I'm not here to pilot Unit 01"

Misato and Ritsuko protested, but Gendo cut them off, "Explain pilot" Shinji clenched his teeth at the insulting assumption that his father would dare to presume that he would his willing tool now but he cooled his passions. Kaji leaned forward and watched interestedly as Shinji continued, "I won't because I don't want to and in all likelihood it won't be needed again"

Gendo snorted, "Boy, just because the Angels have stopped attacking now, doesn't mean they won't attack again"

Shinji answered calmly, "And you're so sure that you made up another scenario, have you?"

The others watched in stunned silence as Shinji defied his father, Shinji! Of all people. Kaji couldn't hide his grin. Gendo and Fuyutsuki stiffened, if statues could have stiffened, until Gendo nodded, "Proceed, pilot"

Shinji wouldn't allow his father to have any satisfaction seeing him uncomfortable, "And thirdly I'm here to deliver a message and to prepare for someone's arrival"

Fuyutsuki interrupted this time; "Do you think we would just let some unknown person waltz into headquarters?"

Shinji growled, "You watch what you say about the person I serve"

Something in his tone made Gendo and Fuyutsuki pause. Wary, Gendo voiced his question, "And who is this person?"

Shinji snapped, "It is none of your concern except that she was the one who disrupted SEELE's timetable"

Kaji's eyes widened at this so did Misato and Ritsuko. Gendo seemed shaken, and Fuyutsuki shifted uncomfortably. Shinji's eyes narrowed as he stared at his father, "Yes, she's told me everything about you, SEELE, Adam, and the Instrumentality project. I must admit it is impressive but very foolish, since it would have destroyed mankind"

Gendo snarled and stood up, "Are you calling my life's work a sham, boy?"

Shinji felt satisfied that he finally got a rise out of father, the others were confused and a bit scared. He sneered, "Your life's work, or do you mean mother's"

A vein began to throb on Gendo's forehead; Shinji realised that he had gone too far. He continued, "The message is that, the Angels have been diverted the moment I left and they won't be coming back for awhile except for one, but he will be freed soon"

Misato and Ritsuko looked intrigued, "Who?"

Shinji answered simply, "The Fifth Child"

The group gasped, even Gendo's eyes widened, "SEELE had an Angel in their keeping, his name on Earth is Kaoru Nagisa but his true name is Tabris. It doesn't matter now, he will be free to join his brethren in Heaven or join us but either way the Angels won't be the instrument of our destruction unless we will it so"

Asuka, Touji and the three techs muttered, Asuka spoke out, "Who and what are this SEELE thing you keep talking about?"

Shinji smiled, "I'm sure my Father or Commander Fuyutsuki can answer that better than I can"

Everybody turned to look at the Commanders, even if some of them knew about SEELE. Fuyutsuki sighed, "I might as well start"

But Gendo cut him off, "Is that wise?"

Fuyutsuki countered, "They know too much anyway, knowing a little more won't hurt, if what Shinji says is true"

Gendo scowled but he nodded. Fuyutsuki cleared his throat, "Well, to begin with SEELE are an Illuminati-like organisation, but their history predates even them, some say that SEELE could trace it's history to the time of Christ but that's just a rumour. You see, it is SEELE who works behind the shadows of almost every major political upheaval in the world, it was them who covered up Second Impact and they now control the UN, and were the ones who ordered the formation of GEHIRN and NERV." To the people to whom this is news gasped in shock.

Misato began angrily, "So we've been working for the bad guys all along"

Shinji interrupts, "Well, actually no, Father here" He smiles almost nastily at Gendo, "Father here, has been trying to stop them or at least delay their plans for mankind"

Gendo sort of nodded, and Shinji accepted it as an affirmative, "Well, there was another…faction that disagreed with Angels' plan for mankind as well"

Asuka bewildered, "What?"

Shinji calmly spoke on, "Well, Asuka. Remember our battle against the ninth Angel, about how I asked why did the Angels attack us"

Asuka and Rei nodded.

Shinji: "Well there was some sort of reason, they were here to test us, a test for humanity itself. How well we were doing I still don't know but I do know that the other faction disagreed with the Angels' methods and stepped in"

Gendo settling into his usual position, "And who compromised this 'faction'?"

Shinji grinned, "Don't worry you'll find out soon when She comes. As I was saying, this faction didn't like the Angels' methods, especially when it involved the innocent, like your sister Touji"

Touji smiled tightly to his friend, Shinji asked a question he's been meaning to ask, "Is she okay?"

Touji: "She's okay but she still having trouble walking and doing normal things. Her injuries were too severe"

Shinji placed a hand over his heart, "Don't worry Touji. She'll be running and jumping again in no time, I promise it. Just make sure she's here this afternoon"

Touji nodded, unsure what to make of this, "Sure, she's coming in to the NERV hospital for a check up anyway"

Shinji: "That's good. Anyways this faction, took the matter up with God himself, and the test has been shifted"

There were a few strangled chokes coming from a few people, including Gendo and Fuyutsuki, "_God_ himself!!"

Shinji shrugged, "I never said that this faction was totally human, but the test will have to go on but this time its going to be fought out in private, so there won't be any big Angels coming in. So pretty much soon, the Evangelions would be useless"

Asuka jumped up at that, "What?! You can't do this"

Shinji rounded on her, "What do mean? I'm not the one doing this, or would you prefer Angels tearing up Tokyo-3 again, hurting people who shouldn't be involved in the first place, people like Touji's sister"

Asuka recoiled from the force of Shinji's words and cursed him and herself, in a quiet voice she said, "But the Eva's all I got left"

Shinji's hard gaze softened, "No"

Asuka lifted up her head, "What?"

Shinji took a deep breath, everybody saw that this was a new Shinji, braver, even more compassionate and wiser. Shinji answered her, "No, you've got Misato, Rei, Touji, Hikari, Kensuke and…and me"

Asuka was speechless, as was everybody else as they all stared at this new Shinji. Shinji perked up; "It's time. Would you all come with me outside"

They followed him through many corridors and escalators, NERV staff watched in amazement at this wild-looking young man leading most of the head staff of NERV. Inevitably some people were drawn along as well, and soon the little group grew to a huge following. Shinji led them out of the pyramid that was NERV headquarters, and into the Geofront, past the lake and atop a hill on the 'floor' of the Geofront. The crowd milled around wondering what the hell was going on. The original group waited expectantly, even Gendo was impatient to meet the one who had enough power to disrupt his plans and SEELE's and even those of God himself. Suddenly the light in the Geofront took on a golden tinge, which was strange since it was the middle of the day. The crowd watched in awe, even Rei was surprised, the only one who wasn't was Shinji.

Shinji smiled happily; "Here she comes"

Soon that golden light intensified, and to the amazement of the people present lines of golden light spread like ripples through the earth. People felt their tensions ease, a wave of contentment and peace spread through them, increasing their wonder. That was when a beautiful purple haired woman, dressed in a flowing white dress, carrying a staff topped with a gold design, stepped up onto the hill before them. The most astounding thing was that this woman was radiating this golden light and the feelings of peace, those who beheld her was simply captivated by the serene power and wisdom she bore in her eyes, as well as the golden aura that surrounded her. Shinji kneeled (on one knee) before her, and she laid a hand on his head in benediction, a short time later he rose and escorted her to where his companions were waiting. As she moved towards them that golden aura faded but that feeling of peace never did. She halted a few paces away and Shinji in a loud voice announced to his companions, "Come and meet the goddess that I serve. Meet Athena, defender of this world"

Most of the crowd instinctively kneeled before her, but Athena stopped them and bade them to rise as it wasn't needed but Gendo snorted, "Don't be ridiculous, Athena is just a myth. She doesn't exist, this is just a sham"

Shinji bristled but Athena stopped him from killing his father right then and there with a brief touch on his arm. Athena spoke calmly, showing no sign that she thought he insulted her, "And what proof do you need to recognise the truth?"

Gendo eyed her, unsure what to make of her challenge, "Grant me my heart's desire"

Athena didn't even bat an eyelash, quietly she responded, "You want to be with your wife again"

It took awhile but Gendo nodded stiffly, as Fuyutsuki gaped at the exchange.

Athena commanded, "Then take me to her"

Gendo's reply was to turn around and walk in the direction of NERV HQ. Shinji followed Athena as she trailed gracefully in Gendo's wake, all the staff overcome with awe, giving way to them. Slowly the crowd followed the wondrous woman and Commander Ikari to the Seventh Cage where Unit 01 was being held but only the original group was allowed in. Shinji had his fists clenched, whether in anger or otherwise, it did not show on his expression. Athena approached Unit 01 via the umbilical bridge, she spoke softly, "It's been awhile since I seen this"

Gendo stood shocked, the others were flabbergasted except for Shinji, of course.

Ritsuko suddenly demanded, "How would you have seen Unit 01?"

Athena turned her head and smiled at the good doctor, "Who do you think was responsible for its disappearance for a few months, after the 13th Angel?"

Jaws dropped and eyes grew wide at this strange woman's answer. Athena turned back to Gendo, "Are you absolutely sure, what you may get, might not be all you expect?"

Gendo tightly replied, "I am certain. I worked toward it all my life"

Athena: "If that's your wish"

She grasped her staff, and closed her eyes; soon she began to emit that soft golden aura. Her hair started rising as if it was being electrified, evidence to the power being used. Slowly she walked around the umbilical bridge until she reached the entry plug port. Of its own will, the head of Unit 01 rolled forward and armour plates retracted revealing the place where the entry plug rests. Athena simply reached into the black hole with a glowing hand, and something responded. Slowly backing away, she pulled out a woman, Misato guessed her age to be mid-twenties, Gendo stood wide-eyed unable to believe the sight before his eyes, she had achieved in a ten minutes what he couldn't in ten years. Gendo dashed over and cradled the unconscious woman in his arms, as luck would have it, his tinted glasses fell off. Everybody present could see his eyes and his tears as they fell. All the NERV staff, including Shinji were amazed at the change in Gendo, as he wept in gratitude, Athena smiled down benignly at him, as he held Yui Ikari in his arms. Shinji hovered beside them, unwilling to intrude on his father's rejoicing Fuyutsuki moved beside him as well. Slowly, oh so slowly Yui's eyes fluttered open, she moaned, "What happened?" Her eyes focused on the face above her, "Gendo?! What's going on here?"

Gendo's eyes shone through his tears, as he clasped her to him tightly, "Everything's okay now"

This time Shinji spoke gently, "Now do you believe, father"

There wasn't a coherent answer from Gendo, but Yui reacted to Shinji's voice, she managed weakly, trying to focus her eyes, "Sh-shinji?"

Shinji knelt and grasped his mother's hand, tears also in his eyes, "Yes, it's me, mother"

Fuyutsuki coughed, "I think we should get Yui into the infirmary"

Athena shook her head, "That would be wise, she needs time to recover mentally, but physically she's fine. Would you please go and get her some clothes, Professor Fuyutsuki?"

Fuyutsuki immediately responded to the command, "Yes ma'am!"

Ritsuko summoned the medics and soon a stretcher arrived, and pried a frail Yui Ikari from the Commander's arms, though some of them were stunned from seeing actual tears in the Commander's eyes.

When the Commanders left with the medics

Athena: "Shinji, was there someone else you wanted me to meet?"

Shinji: "Yes" He turned to Touji, "Can you take us to see your sister?"

Touji nodded, unable to speak. Walking carefully as if the ground was spinning under him, he headed towards the NERV hospital, with Shinji, Athena and their companions in his wake.

Touji: "Mari? We have some visitors"

A young, brown-haired girl looked up from her book: "Onii-san!"

Getting up awkwardly, she struggled out of bed and slowly stumbled her way to her older brother. Touji lifted up his younger sister easily, and placed her on his shoulder, the young girl squealed happily. Shinji shuffled in awhile later.

Shinji: "Hello Mari!"

Mari: "Shinji!"

Shinji smiled slightly, "Long time no see"

Mari squinted at him: "You changed, Shinji"

Shinji grinned ruefully, as Mari reached over and tugged on his shoulder-length hair.

Shinji: "I brought someone to see you, Mari. She can make you all better, and you can run around again"
Mari looked at him, eyes shining hopefully: "Really"

Shinji nodded, and shuffled aside to admit Athena.

Athena: "Hello Mari, you can call me Saori-san"

Touji looked at her quizzically.

Shinji: "I'll explain later"

Mari tried to bow from where she was sitting: "Hello, Saori-san"

Athena: "Shinji tells me you got injured and it's his fault"

Mari shook her head: "No, it's not. He did everything he could to save us during the attack, it was the Angel's fault"

Shinji turned away so nobody could see his tears, Athena smiled serenely at the young girl.

Athena: "Can you place your sister onto the bed?"

Touji moved quickly to comply, placing his sister gently onto the bed. Athena laid her hand on Mari's forehead, and started glowing again, slowly the golden aura spread from her hand to Mari's body, til it totally infused the young girl. Mari watched in wonder, as the golden glow receded, and her legs twitched without pain. Gingerly she moved her legs over the side the bed, and touched the ground. She gasped; there was no pain.

Athena smiled: "You're all healed now, Mari"

Soon another step followed her first, and within a few steps she was running. She jumped into Touji's arms, who was crying, sharing his sister's joy as both siblings hugged each other.

Mari broke the hug, and rushed over to Athena and hugged her too.

Mari: "Thank you, Saori-san"

Touji breaking down: "Thank you"

Athena: "Your thanks is not needed. It is my pleasure to see both of you well"

Athena and Shinji retreated out of the room, to leave the brother and sister alone.

Athena: "I hoped that has helped"

Shinji: "Y-yes, Saori-san. I suppose it had"

Athena: "Don't worry about it. Everything is now all right, except for the final battle. You have the strength to see this through, just believe in yourself"

Shinji: "That's easier said than done"

Athena: "No, Shinji. That's what you think. I'll have to go now, until it's time again"

Shinji: "I understand, I'll go see you out"

Athena laughed lightly: "You don't need to. You really should get back to your friends, you have some friendships to renew"

Shinji shook his head and insisted on accompanying her, at least to the Geofront. Athena glowed softly and disappeared into the golden light, which soon faded afterwards, no trace of her presence anywhere. Shinji stared at the spot where his goddess was; he was suddenly woken from his reverie by a hand on his shoulder.

Misato: "Shinji, you should go get some rest. It's been a hectic day"

Shinji stifled a yawn: "Not yet. I still gotta go see Mother"

Misato: "She'll still be in her hospital room. Go rest"

Shinji: "Maybe, but I'll go see her first, okay"

Misato recognised that tone, it was his stubborn tone, he used it rarely but she recognised it all the same. So she gave up and led him to the hospital room that his mother was in. Shinji knocked once, and went in. Surprisingly his father wasn't there, but his mother was, lying on the bed. His breath caught as she stirred and opened her eyes to look straight at him.

Yui spoke weakly, "Shinji?"

Shinji swallowed the lump in his throat, "Mother"

Yui raised her arm weakly, "Come here, my son"

Shinji clasped his mother's frail hand, even though her body was weak, her mind was still sharp, she noticed the number of calluses on her son's hand. Shinji choked on his tears as the feelings he was holding back before broke free.

Yui spoke softly trying to comfort her son, "Don't cry now. I'm back. Everything's okay"

Shinji's tears stopped as he responded the motherly tone, and embraced the blissful oblivion.

Misato asked anxiously, "How is he?"

The doctor cleaned his glasses, "Well, physically he's fine if not great, but he's exhausted. And with the hectic events today, his mental condition took a few blows, so he's exhausted mentally as well but with some good rest, he should be fine"

Asuka jumped up from her seat; "Can we see him now?"

The doctor looked unsure but seeing the expression on Asuka's face, he couldn't refuse, "All right. Just don't wake him up"

Asuka and Misato walked in quietly, careful not to disturb the sleeping figure on the bed. Shinji lay on the bed, covered up to his chest by the sheets, his longish hair spread out around his head. Unknown to the two, Rei had also stepped into the room.

Rei spoke in her quiet tone, "How is he?"

Asuka and Misato jumped in surprise, and both women turned around to face Rei. Asuka was close to an angry outburst, but Misato shut her up, and answered Rei, "He's just exhausted, he'll be fine"

Rei: "Oh"

Misato smiled warmly at the young woman, who shyly approached the bed.

"We all missed him"

Rei was surprised, as was Asuka.

Rei answered, "Yes, I did"

Asuka remained silent, unsure what to say.

Then Shinji surprised them all by waking up, bolting up from the bed with a gasp. He was panicking, as Rei and Misato tried to subdue his flailing limbs. Asuka, for some reason, slapped him hard, Shinji shook his head, and his eyes focused. Breathing heavily, he asked, "What was that for?"

Asuka sniffed, "I was merely helping. Look at how ungrateful you are"

Shinji worked his jaw and replied dryly, "Most people don't tend to try breaking someone's jaw, in order to help them"

Asuka shrugged, "Depends on your point of view"

Shinji looked at his arms, which Misato and Rei was pinning to the bed, "Misato, Rei, I like my arms back now"

They released him and he swung his legs off the side of the bed.

Misato admonished, "Shinji, get back into that bed this instant"

Shinji looked at her quizzically: "Not now, Misato. Not with Asuka and Rei watching, unless…"

It took her a moment too long to process that, by then Shinji and Asuka were laughing, Rei had a small smile, which meant she was really amused. Shinji fended off Misato's playful swats; "It's really nice to be back"

Rei smiled at him, "It's nice to have you back, Ikari-kun"

Asuka and Misato stared at the unusually talkative Rei; Shinji seemed astounded, having heard the most words she had ever spoken.

Shinji got to his feet, up close to changes to him were more evident to the three women he had shared his life with. Physically he was taller, a bit more muscular; his face kept some of its boyish charm but had taken a rougher look, as if he had been sunburned many times. If his clothing was anything to go by, then he had been living rough, which was strange, since he didn't know any survival techniques before he disappeared. However his presence excluded a cold, unemotional calm, and only Rei noticed that the temperature of the air surrounding his body seemed to be a few degrees cooler. Misato saw a difference in his behaviour, he had a…steadiness to him, a sort of quiet competence, and confidence that he didn't have before. Asuka saw a familiar but different Shinji, one that had grown up from the wimpy thing that she knew from before, some of his original shyness was still there, but it was tempered with strong willpower and something else, but Asuka couldn't quite put her finger on it. But they were suddenly interrupted by screams from outside; Misato immediately whipped out her pistol and positioned herself beside the door. Shinji surprised them all by opening the door and stepping outside into the hallway. Misato cursed, and yelled at Shinji to come back into the room, while the girls stayed behind Misato.

In the hallway, Shinji stood alone, wondering what happened to the staff after the initial scream. That was about the time he realised that it was a trap, ten big men rushed out of adjoining corridors at him, but surprisingly none of them were waving guns or firearms of any sort. When they were metres away, Shinji realised who they were, guards clad in antique armour. Yelling a war cry the first two reared back and threw punches at him, which he ducked to avoid, simultaneously running a fist into the stomach of one. That one folded up around his fist, spittle spraying from his lips, with remarkable speed, Shinji spun around and leapt at the man behind him with an outstretched fist. A solid crunch, and the man was down, metal helmet shattered, another punch sent another into the metal wall, leaving an imprint of the man. Shinji grabbed the arm of another throwing a mailed fist at him, and used the momentum to throw that man headfirst into the face of another oncoming. A bone-cracking impact later, Shinji sent the seventh sliding down the hallway, leaving a trail of blood. The eighth stood no chance, with an uppercut, that deformed his jaw, and had enough force to crush his skull on the ceiling. The ninth tried a waist-high tackle, but Shinji flipped over him agilely and punched him hard enough, that he rebounded off the ground and into the ceiling. This had only taken one minute. The tenth was wiser; he was wielding a short spear, and had better-maintained armour, Shinji guessed he was the leader.

Goon leader sneered at him; "You won't be able to beat me so easily"

With that, the man lunged at him, spear flickering in front of him, Shinji managed to dodge the spear but not the armoured fist sent his way. Shinji stumbled and the man was about to finish him with the spear, before the spear point reached Shinji's throat, a gun went off and the haft snapped, the spear point bounced away. Shinji shook his head, and hit the shocked man between the eyes. The punch didn't kill him but it did shatter the front part of the helmet the man was wearing, the man collapsed bonelessly. Shinji turned around to find Misato pointing a gun at him, Shinji was taken aback.

Misato, gun steady: "Who are you?"

Shinji was confused: "I'm Shinji, Shinji Ikari"

Misato gestured with her gun: "The Shinji I knew couldn't do that"

Shinji looked around guiltily: "I'm sorry, I do not like taking human life but they are trying to stop me from doing my purpose"

Misato: "That doesn't tell me anything, for all I know, your purpose could be to destroy us all"

Shinji raised his hands, with palms open: "Look at me, Misato. I am Shinji, the Shinji you knew, and a Shinji that you don't. I have changed, for the better or worst, I have changed"

Misato's resolved swayed, this sounded like the introspective boy she had known, but…

Shinji got close enough to grasp Misato's pistol, holding onto the barrel, "Misato, it's all right. It's me"

Asuka: "Stop it Misato!"

Misato dropped the gun; it clattered onto the floor noisily, her shoulders sagging as well. Rei caught her before she fell,

"Ikari-kun, what happened?"

Shinji understood her immediately: "I'll tell you later. Let's get Misato comfortable first"

Together they carried the older women to the bed that Shinji had formerly occupied.

Yui Ikari's voice: "Could somebody explain to me why there are dead bodies outside?"

Shinji turned around: "Mother! What are you doing here?"

Yui looked exasperated: "Isn't a mother allowed to see her own son?"

Shinji coughed, trying to hide his embarrassment.

Asuka: "You seem to be taking this awfully calm, Mrs. Ikari"

Yui dryly: "When you've seen what I've seen, dead people aren't that impressive. You must be Asuka"

Asuka: "Yes, how did you know my name?"

Yui: "When I was part of Unit 01, Shinji left a very strong impression when he was piloting, I could perceive some of his memories"

Shinji started: "My memories?"

Yui hugged him and in a soothing voice: "Don't worry, it was nothing too private"

Shinji returning the hug: "Oh, how have you been, mother?"

Yui smiled: "So and so, I don't look a day over 26, so I'm not doing too badly for a woman in her late thirties"

Misato: "Shinji, you have some explaining to do"

Yui smiled warmly at the purple-haired woman: "You must be Major Katsuragi. I am in your debt"

Misato was taken aback: "About what, Mrs. Ikari"

Yui: "For taking care of Shinji when he stayed here in Tokyo-3, he saw you as a mother-figure, you know if a messy one"

Misato: "It was my pleasure really. It was nice to have a family"

Asuka: "That's sooooo sweet"

Yui laughs as her gaze traverse the room, where it falls on Rei, shock painting her features.

Asuka follows Yui's gaze, and swivels her head back and forth between Rei and Yui: "Misato, is it just me or do they look a lot alike"

Misato cleared her throat: "Mrs. Ikari, meet Rei, Rei Ayanami, the First Child, and pilot of Unit 00"

Yui: "And a child born from my DNA"

Misato, Asuka and Shinji goggled at her.

Rei quietly: "Yes, that is true, I'm a partial clone made from your DNA. The Commander created me for his plans"

Yui: "Rei…that was the name we were going to give our child if it was a girl. I'm going to have a long talk with my husband"

Misato thought to herself, 'Wouldn't I like to see that"

Asuka silently, 'I always knew Wondergirl was messed up, but not this much. No wonder'

Shinji: "So does this mean she's my sister"

Yui/Rei: "Sister…?"

Shinji watching Rei intently: "Yes, if she is partially made from your DNA, mother which means she shares my DNA and therefore we are brother and sister"

Rei's gaze shifted from Yui to Shinji: "Brother…?"

Yui looked uncomfortable: "Well…from that perspective, yes. Technically…I'm not so sure"

Gendo's deep voice interrupted her: "Well, yes Shinji, Rei can somewhat be considered related to you but…"

Shinji's expression shifted to an icy one, he spoke somewhat stiffly: "Gendo"

Misato thought she could refrigerate her beer with his tone.

Gendo looked pained: "I understand that you're mad at me, but…"

If it was possible, Shinji's expression grew even icier; Gendo could feel a chill in his bones.

Shinji: "Mad doesn't begin to describe it"

Yui stood between the two: "Shinji, please"

Shinji relented in the face of his mother's distress: "Yes mother"

He turned his back on his father to find a chair to sit on. Rei's eyes narrowed with interest as Shinji sat down, something was affecting the temperature slightly, and Shinji was the most likely cause. Studying Shinji intently she wondered why he was sweating, despite the hospital environmental control, and then she turned her attention back to the woman who's DNA she was cloned from and the man that had given her life.

Yui in a steely voice: "Gendo Rokubungi, I'm going to have a few words with you later, in private"

Gendo visibly winced, to the amazement of all gathered in the room.

Yui: "But first, will somebody tell me about the dead bodies outside"

Shinji: "Easy, I killed them"

Yui and Gendo looked stunned: "What…How?"

Shinji readjusted the wrappings on his left arm: "I used my hands"

Misato: "Yes, he did. We saw it with our own eyes; he eliminated all ten of them"

Shinji: "Nine, I left the last one, I wanted some answers"

Gendo: "I'll get security to clean up the mess and hold the man until he's ready to talk"

Dialling on a cell phone, he quickly made the call.

Yui/Misato: "Shinji, I think it's time you explained everything to us"

Shinji: "Why? You've met most of the reason"

Gendo: "You mean Athena"

Shinji: "Yes, she's the reason for a lot of things"

Misato began angrily: "That doesn't tell us anything!"

Shinji shot out of his seat and stared her down: "No, it might not but that's all I'm willing to tell right now"

He turned away and walked to the window, seemingly looking out at the scenery.

Rei walked over to him: "Ikari-kun"

He took a shuddering breath: "Sorry, but you wouldn't understand what I went through"

Rei reached to touch his shoulder, then jerked her hand away as an intense cold burned her hand. Shinji spun around, anguish present on his face.

Shinji: "I'm so sorry. Are you hurt?"

Rei: "No, it was more of a shock"

Shinji: "I'm sorry but I can't tell you everything, you wouldn't understand"

Asuka scowled: "You're still as stupid as ever, you haven't changed one bit"

Shinji: "Neither have you"

Asuka paused in mid-rant and started blushing.

Shinji: "It's a comfort to know not that much has changed"

Misato: "Shinji, you're not leaving this room until we get some answers"

Yui: "Yes, Shinji tell us what happened"

Shinji: "I said you wouldn't understand. Now would you leave me alone?"

Yui snapped: "Shinji, tell us what happened NOW!"

Shinji winced: "Yes mother"

Despite some changes, Shinji still had some old habits to break. Shinji sat down heavily as the group gathered to hear him out.

Shinji: "Well, it started four years ago, when I disappeared"

Asuka: "Well, duh"

Shinji gave her a look: "I was given a choice; to see humanity die or help save it, you had no idea how hard that choice was"

Asuka: "What are you, stupid? How hard could it be?"

Shinji's tone was arctic: "Be quiet, Asuka. You wouldn't know how I felt that day"

Rei: "The day where the dummy plug almost killed Pilot Suzuhara"

Shinji flinched, as well as Gendo when Yui gave him a look that should have left him bleeding. Shinji closed his eyes and sighed, "Yes, but in the end I made a decision and I was trained. For four gruelling years I trained, day in, day out, in a land that was bleak and unforgiving but it had its measure of kindness, there were no lies, no deception. I learned many things there, in my heart it became a home, a place I could feel secure, despite the dangers it held, when it was time I came back"

To Asuka's opinion that fell short of an explanation, but the others didn't push for any more information, they could see that they won't get anything else out of the young man until he was willing to share it.

Shinji: "Misato?"

Misato trying to comfort him: "Yes, Shinji"

Shinji: "Where will I be staying?"

Misato looked around uneasily: "Well, I thought you might want to stay with your mother"

Yui: "I don't even know where I'm staying tonight"

Gendo sounding unsure for the first time: "Um, there's room for one more in my quarters"

Yui: "We'll talk later, IN PRIVATE"

Gendo gulped nervously: "Yes, dear"

Misato: "Your room is still there, waiting for you"

Shinji stared at her: "You kept my room"

Misato: "Yes, I believed you would return one day"

Shinji: "I don't know what to say except thank you"

Misato smiled: "You're welcome, Shinji. I'll cook tonight"

Shinji sweated: "Eh, no. How about I do it?"

Misato's smile just got wider: 'Yes!' "Okay then, fine by me"

Asuka grinned: 'Alright, real food!"

Shinji: "Oh, by the way, can my sister join us?"

Misato: "Huh, Rei? Sure, why not? The more, the merrier"

Rei: "I don't want to impose"

Misato: "It's all right"

Shinji: "Rei, do you still live the same apartment"

Rei: "Yes"

Shinji gave his father a frozen stare: "Then you can live with us until this is all sorted out"

Asuka: "No way!"

Shinji glared at her, and she glared back, Misato watched as neither seemed to blink. After some considerable time…

Shinji: "I think my eyes dried out"

Asuka: "Mine's too. It's all your fault"

Shinji: "You're the one arguing"

Asuka: "You started it"

Misato rubbing her temples: "Enough, children! Rei's coming with us. Mrs. Ikari, will you join us?"

Yui: "Call me Yui"

Misato: "Alright then, Yui. Want to dine with us?"

Yui: "As much as I love to, I can't. I've got a few things to sort out, how 'bout some other time?"

Misato glanced at Gendo: "Alright, then we'll take our leave of you, I'm sure you have a lot of catching up to do"

Asuka and Rei made their goodbyes politely, but Shinji hugged his mother before glaring coldly at his father, Yui sighed. She turned to Gendo: "Your son hates you, you know"

Gendo turned his eyes away: "I know, and I understand"

Yui: "Then why?"

Gendo: "I couldn't live without you. I mean really live, for the past sixteen years I went through the motions of living but I didn't really live. Life without you was empty, bleak; there was nothing for me except to get you back"

Yui: "But you could have lived, you could have lived for Shinji, our son"

Gendo: "He wasn't you, Yui! You were and still are the one who could see me for me, not the Commander or whatever they think I am"

Yui sighed: "He could have, if you weren't so blinded, he could have been the one. I chose to test pilot so I could help create a better future for him, but you put my efforts to waste, Gendo. You alienated him, rejected him, at first he thought he could understand but slowly he began rejecting you, he hated you, I was scared when I sensed some of that hate, it wasn't a hot tantrum, it was cold, a rage. Your son developed a slow and terrible temper, and you managed to rouse it, I can see it in his eyes, if there wasn't anything holding him back, he would have ripped you apart"

Gendo drew a shuddering breath: "I only wanted us to be a family again"

Yui: "But did Shinji know that"

After a tour of Tokyo-3's streets, Misato-style, they finally arrived at Misato's apartment. Once the car stopped, Shinji literally leapt out of the car, landing at least fifteen feet away. How could he have been so stupid! All the things he had done in exile could not prepare him for Misato's driving, there was absolutely no way he was ever getting in Misato's car again.

Misato climbing out of the car rather sedately: "Shinji?"

She popped open the latch to backseat so that Asuka and Rei could climb out. Asuka was as pale as Rei and both had a greenish tinge to their features. Asuka's knees wobbled and collapsing slowly on the ground, she kissed it, "Oh lord, terra firma I love you"

Misato: "Come on, my driving isn't that bad"

Rei looked at her curiously, while trying to calm her heart rate. Shinji stared at Misato in disbelief, "Normal people don't drive at 90mph around a corner"

Misato shrugged, "We're still here, aren't we?"

Rei: "I believe that most people don't suddenly drive off the side of the highway, down a hill and into opposing traffic on a one way street"

Misato: "But that's a shortcut"

Shinji: "Next time I'm walking"

Misato: "It's quite far to HQ"

Shinji: "It's no problem; I used to walk to Headquarters anyway"

Asuka and Rei nodded, Misato huffed angrily. Shinji ducked into the backseat to grab the bag of groceries they got surprisingly nothing was broken or spilled.

Within a short time, Shinji had whipped up a quick meal for everyone. Misato and Asuka were glad that his absence had not affected his culinary skills as they sighed gratefully, their first real home-cooked meal in years.

Misato: "That was great"

Asuka: "Yeah, a real meal"

Shinji shook his head: "Didn't you guys learn to cook while I was away?"

Asuka: "What did you think, dumpkopf?! When you ran out on us, Misato took over the kitchen"

Shinji: "Sorry, but I remember leaving at least one cookbook in the house"

Asuka snapped at him: "Well, it wasn't very useful"

Shinji: "Sorry"

Right, Shinji still hasn't gotten rid of that habit, which infuriated Asuka even more.

Asuka: "And stop saying sorry!"

Shinji: "Sor…um, never mind. So Rei, what did you think?"

Rei smiled slightly: "It is better than the Major's cooking"

Shinji grinned, when Misato spluttered into her beer.

Misato: "Rei! What have I told you? You don't need to address me as Major all the time!"

Rei: "Yes, Major"

Misato scowled, but Asuka and Rei smiled in amusement. Shinji wondered if this was some sort of in-joke that he was missing out on.

Shinji: "What's going on here?"

Asuka and Rei grinned, but Asuka answered.

Asuka: "Nothing much, it's just Rei teasing Misato"

Shinji blinked and wondered if he heard right, 'Rei teasing Misato. What's going on here?'

Misato: "Well, Rei's been growing up lately; she's changed a bit from when you last saw her"

Shinji was disheartened that he missed all that, but he was glad, that Asuka and Rei were getting along occasionally even though Asuka still harboured some resentment towards Rei.

Misato licking her lips: "Shinji, now that I think about it, you've grown up into something yummy"

She leaned over, revealing quite a bit of her body, Shinji blushed.

Asuka: "Hey! Get away from him!"

Misato turned around and smirked: "What's the matter? Jealous?"

Asuka's face reddened: "No, why should I be? I just don't want to see something perverted happening"

Rei also blushed: "I concur; I do not believe your advances on Ikari-kun are wise"

Misato smirked: "Is little Rei, defending her brother?"

Rei's blush deepened, spreading down to her neck.

Rei in a quiet voice: "Y-yes"

Misato giggled, at their expressions, before launching herself at another beer.

Shinji felt something hard poke into his side, looking down he saw a yellow beak.

Shinji: "Hello Pen-Pen, how have you been?"

Pen-Pen: "Wark! Wark! Waaaaark!"

Shinji laughed: "I see you're glad that I'm here to cook for you again"

Pen-Pen: "Wark!"

Pen-Pen waddled off to his refrigerator, and retired.

Shinji: "That was a nice welcome"

Asuka: "More than you deserve, baka! I'm going to take a shower, AND IF YOU PEEP YOU'RE A DEAD MAN!"

Shinji just shook his head as he cleaned up, with Rei helping him. As Rei was helping him with the dishes, he decided that it was time that they had a talk.

Shinji: "Rei, how do you feel?"

Rei: "I am fine"

Shinji: "No, what I mean is. How do you feel being my sister?"

Rei: "I am…unsure. I do not fully comprehend these feelings"

Shinji: "That's all right; you'll figure them out eventually. I have faith in you"

Rei blushed: "Thank you"

Shinji: "You're welcome, imoutochan"

Rei smiled slightly as she tried to cover her embarrassment. Shinji laughed lightly, it was good to be the one not being teased. Asuka overheard the exchange; she shook her head and went to have her shower.

End part 2

Sorry, Shinji/Rei fans, they won't be a couple in this story, as much as I like Shinji/Rei pairings, this story ain't suitable for them to be a couple, I think. I'm still thinking on how this story will go, if you have any ideas on improving this story, tell me.