Neon Genesis Evangelion: From the Darkness

By DarkShadowX

Disclamer: I do NOT own Evangelion, Gianax does, nor do I own Ill Gill, that belongs to the good people of Sonic Team. I do own Kai, however (at least I think I do)

Prologue: Swallowed by Darkness
Japan 2004

The people at Gehirn are busy preparing for the awaiting activation test of their new weapon, the 'hope' for humanity.

"How is everything going for tomorrow's test?" asked Professor Fuyutski.

"Everything is going well," answered one of the techs working on necessary data for the test, "we'll have everything prepared for tomorrow's test."

"Good, who will be test piloting it?" Professor Fuyutski inquired.

"Who else but its creator?" a new voice answered, the voice of Dr. Naoko Akagi, "I don't think he would have it any other way, his father DID design it in the first place."

"I suppose not, but are you sure he can handle it? He's still young and he's been through so much stress since his family's death." Fuyutski with a bit of concern in his voice, 'We have no idea what may happen, this is all new after all, we haven't even tested Unit-00 yet'

"Who knows if he can handle it, but you know once he makes up his mind, he won't change it, especially when it comes to anything that has to do with his father's research", retorted Naoko.

"Yes, he much like his father in that respect", Fuyutski saying with a defeated sigh.

"Haha... how true, but I honestly believe he can make it work, it's his gift, he can make anything happen with good effort, just like his father.... And his mother in that regard." Naoko said with slight sadness.

"Yes, he received the best from both parents, well I guess there's nothing we can do except wait. If this works, then we can continue with Project E with full confidence." Fuyutski said. "Well I must be going now, tomorrow is the big day after all, farewell Naoko and good night."

"Take care professor, see you tomorrow", Naoko answered.

With that Fuyutski left with one thought running through his mind, 'I hope he's truly ready, we don't know what can happen, if anything happens to him Yui nor Gendo could ever forgive themselves, he's been a son to them since his parent's death, and young Shinji would be crushed, losing his brother, he's grown so attached to him just like his parents.'
At the household of Yui and Gendo Ikari, they are enjoying dinner with their 2 sons. But. You can feel the tension, as there is still the matter to discuss with the older of their 2 children, the person that had been recently discussed about at Gehirn.

"Kai are you sure you are going through with this?", Yui asked, concerned for her son, "we still have no positive confirmation that you will be safe, or that there won't be any side-effects from the nerve and mental connections."

"Yes mother, I'm positive, this was everything my father was working on and I intend to not just be there to watch it, I intend on being the one who gets it to work." Kai answered with a slight forcefulness in his voice.

Sighing Yui answered, "I suppose there's nothing I can do to make you reconsider. Fine, I won't try to convince you otherwise, but that still doesn't mean I'm not against the idea of you being the test pilot."

With a slight smile Kai spoke, "Thank you mother, don't worry I've checked everything and Akagi-san as well, nothing will go wrong I promise."

"We still want you to be careful, we love you and can't help but worry", answered Yui with a sincere motherly tone.

"We'll be watching the test, so we'll make sure nothing does go wrong Kai", spoke Gendo, "but lets hope it doesn't come to that, I have great faith in your father's work and yours as well, your father would be proud at how far you gotten, especially for one your age."

"Thank you mother, father, I won't let you down and I won't let my father down either, I know things will work out perfec..."

"Are you gonna go pway wit the wobot onii-chan", young Shinji interrupted excitedly.

Smiling at his younger brother, Kai answered, "Yes I am, we finally put it together so now we're gonna try to get it to work tomorrow. Do you wanna come and see it?"

"YES!!!!" yelled a now excited Shinji.

"Kai, you know we can't do that, Gehirn isn't some daycare", retorted Gendo.

"Just this once father, I'm sure Shinji will behave, for me, please", pleaded Kai.

"Pweeze daddy", pleading as well, backing his brother up.

"sigh Very well, but just this once since tomorrow's your big day", answered Gendo after noticing the look his wife was giving him, Gendo was a strong-willed and smart man but even he knew when he was defeated, particularly if his wife was against him.

"Thank you father"/"Thanks daddy!" spoke Kai and Shinji at the same time.

Later that night....

"Onii-chan", Shinji spoke, asking if his brother was awake.

"Hmm what is it Shin-chan" asked Kai slightly tired as he had just fallen asleep.

"Can I sleep wit you, I had a nightmare", Shinji answered sniffling a little.

"Sure, come here Shin-chan", Kai said, slightly worried as Shinji rarely had nightmares, and the ones he's had are slightly bad, well as bad as it can get for a 3 year-old, "do you want to talk about it?"

Sniffling, Shinji spoke, "I saw you go into the big wobot, but then something happened and everyone started yelling and then this big black thing came and ate you and you never came back", tears started coming from his eyes.

Kai was shocked, this was a first as none of Shinji's other nightmares were nothing like this, seeing his reaction slightly worried him. He knew that Shinji was actually pretty intelligent for his age, his ability to speak almost fluently and ability to comprehend most situations a child his age couldn't is proof of that. "Don't worry Shin-chan, I'm right here and nothing bad is going to happen tomorrow, I promise, now come here and lets get some sleep." He then pulled his little brother into an embrace and into bed where Shinji quickly fell asleep.

He was still a little worried and continued to watch Shinji sleep. Ever since Shinji was born, he was instantly attached to him just like a real big brother to his younger one. Yes a real big brother, but Shinji doesn't know the truth. Kai Ikari is not related to them by blood, his true name is Kai Shiatori, his family were great friends to both Ikaris. Of course, Second Impact changed everything, it had killed his entire family father, mother, brother, uncle, you name it they were all dead, he was the only one left. After their death the Ikaris took him in and adopted him. After that they became very close well at least him and Yui, he and Gendo didn't necessarily become close but they were still on friendly terms, and that closeness became even greater with the birth of Shinji. Even though he knew they weren't related by blood, that didn't stop Kai, he had a new family and he wouldn't take any of it for granted. Shortly before Shinji's birth, he had begun from where his father left off. One would think it was impossible for an eleven year-old to continue this kind of research, but he had been around this research his entire life, his mother and father highly respected professors and his older brother a highly respected scientist. The research was to be used to save humanity from the future threat of the Angels and being a young child with a highly used intellect, he paid close attention to their research. Unlike most children, he was home schooled by his family and learned extremely quick, in fact he was already at a Second Year College level by the age of 8. After he had accepted and dealt with his family's death, he helped complete his father's research and built his creation, Ill Gill, a biomechanical robot, or cyborg according to Dr. Akagi, which was also the basis for Evangelion Unit-00, the prototype model, he found it slightly funny that his Ill Gill was a prototype for another prototype. Because of that fact he also helped with Project E and the construction of Unit-00, though there are major differences between the two, the only thing in common was the Plug System and they also shared similar physical designs, though they still highly differed, and they also shared the fact that both possessed cells from the First Angel, Adam, a fact he was slightly against in the beggining and still is to an extent.

Kai soon began to succumb to sleep, he knew he needed it though for tomorrow's activation test, if the test is successful they will be able to test Unit-00 without any fear and then begin construction of Unit-01 which will be designated the test model, but something inside him told him Unit-01 will serve more than just the test model, perhaps it was from the fact that Unit-01 possessed cells from Lilith, the Second Angel rather than Adam's cells. He also got this feeling whenever he saw Shinji, he knew Shinji is destined for great things but he prayed and hoped it would have nothing to do with the Evangelions or the Angels for that matter, he wouldn't forgive himself if Shinji somehow became involved and worse if something happened to Shinji cause of his involvement. With that Kai finally went to sleep with one last thought, which he spoke aloud, "I hope your dream doesn't come true Shin-chan, I won't abandon you, I stake my life on it."

Silently watching, Yui had heard everything that occurred in that short time. 'I hope nothing happens either, I could not bear to lose either of you.' With that Yui returned to her room to sleep.
Gehirn, day of the activation test

Tensions were high today, as the big day has come, the activation of the Shiatori's creation, Ill Gill, and with its activation it will officially start Project E.

Exiting the locker room, Kai came out in an all black plug suit, which he doesn't like, as it's skin-tight and makes it somewhat uncomfortable since it seems a bit small for his toned body, which is thanks to his martial arts training he took up after he finished his education. He had his blackish-brown hair hanging down to his shoulders, as he couldn't have it in his usual ponytail for the test, black A-10 neural connectors clipped on, which he too finds it kind of annoying to have on. All in all it's easy to say he likes black, from his hair to his plug suit and the neural connectors to his eyes, though his eyes are more like a dark black with a hint of blue in them, some people say one could easily get lost in his eyes, as if they can bore deep into one's soul. He then makes his way to the Prinpow Box where everyone will be monitoring the test.

As he enters, his young brother instantly tackles him. "Good luck wit the wobot onii-chan!" Everyone watches the scene with a smile on their face, but they are also filled with concern, not because if the test fails they have to do even more work, but they don't know what may cause the test to fail and what could happen to Kai because of it.

"Thank you Shin-chan, I'm sure everything will go well, and I promise that once this is done we'll get some ice cream and go to the park."

"Well you better get going, I'm proud of you son and I'm sure your family would be as well", Yui said with a tinge of worry in her voice.

"Thank you mother, and everyone else here for making this possible, this test isn't just for me and my family, but for all of you as well because without any of you, this would have never happened." With that Kai went to the Umbilical Bridge as everyone said their thanks and good lucks.
As he reached the center of the bridge he looked at Ill Gill in all its magnificence. He started at the thirteen or so stories high machine with a sense of purpose. Ill Gill truly was something to behold, aside from its obvious size, it indeed looked intimidating. It was a dark black color, shaped like a human, it had a human shaped head with a single blackish-white horn that extended from the back of its head, the face had a single red visor and a silver metallic colored mask covering where the mouth would be (if it really had one). It also had a chest plate of sorts, more like a body armor that covers the chest, back and shoulders. What it is in truth is an armor/jetpack sort of thing, the chest and back area of it are a silver metallic color, while the shoulder part looks more like a giant shoulder pad of sorts is a dark black while the ends of it are again a metallic silver. The back area as said before is a silver metallic color, the design is simple in which if covers the back but also has two fin-like extensions that continue slightly at a downward angle, but not sticking out like a fish-fin. But between the body and the back armor covering is where the jet propulsion engines are, though it has these they are not specifically used for flight, though it is capable of it, they are used to increase Ill Gill's speed, if when on it's field activation is successful, will make it appear to float across the surface at high speeds. Also on it's back, is it's only visible weapon, a large metal staff but at the end of it, there is a small energy generator which generates a heat blade which then makes the staff look more like a scythe. It's other weapon is a pair of Progressive Knives hidden in its shoulder compartments, though they've been completed they have yet to be fully tested.

Kai takes one last look, then proceeds to enter the entry plug. Once inside it is filled with LCL, 'I still can't get used to it, not matter how hard I try to ignore it, it still tastes and smells like blood' Kai thought sourly. The entry plug is then inserted into Ill Gill from the back between the neck and the spinal column, as Kai prepares for synchronization, which he knows will be very different from the simulation tests in the simulation plugs.
Everyone in the Prinpow Box watches in anticipation as the synchronization process begins. Soon they go through all the stages and begin to reach the borderline, which is where synchronization will take place.

"Borderline reached... he did it he passed the borderline. Synch ratio currently at 47.88% and holding", answered one of the techs.

"Amazing, in the simulations he barely made 18% and just like that he's almost 50% synchronized", said a surprised Dr. Akagi.

"Well, Kai's been waiting for this moment his entire life, and Ill Gill is his family's work, so its understandable that he would have a higher synch ratio in it than in the simulation plugs", spoke Yui truly happy that everything is going well.

"How true Yui, we should have expected this from him, he has proved us wrong many times I, myself, would have expected no less from him, he is after all Shiro's and Mai's son", spoke Prof. Fuyutski.

"Well enough praise", Naoko hits a button and speaks, "How's everything going Kai?"

"Everything is going fine, no problems."

"How do you feel", said Naoko with barely noticeable sound of concern in her voice.

"I feel great, my senses feel like they be heightened, though my body does feel a bit out of place, but that's to be expected from synchronization."

"Yes how I suppose it is, well all in all I'd call this test a success, wouldn't you Kai?"

"Yes, everything went just fi........ AHHH!"

Kai suddenly began to scream in pain as everyone tried to figure out what is going wrong. "What the hell is this it's not possible?" one of the techs suddenly said.

"What, what is it!?" shouted Naoko.

"Kai's being rejected by Ill Gill, but his synch ratio keeps on increasing, it's jumped to 96% and is still climbing at a fast rate."

"That's not possible, his synch ratio can't increase if he's being rejected!" Naoko yelled.

Inside the plug, Kai is clutching his head, feeling like it's going to explode. Pain is all he feels, but through the pain he hears an ominous and frightening voice speak to him in his mind, 'to be one, to be one, to be one.' The voice continues to repeat as Kai feels his senses dulling, as if his body is being separated from his mind.

"Oh my god!! His.. His synch ratio is at 400%!! What the hell is going on how can this be possi..." the tech starts saying as he is interrupted by another tech.

"We're getting a reaction something is happening!!!"

They all began to watch in horror as an orange hexagonal shaped light seems to come from Ill Gill, what has been recently been identified as an AT Field.

"That's not possible according to Kai's and our research, Ill Gill shouldn't be able to generate an AT Field", Naoko said in horror as she continued to watch the events unfold.

Through all this, young Shinji also watches in horror, the same feeling of frightening emptiness he felt from his nightmare begins to manifest itself within him. He knows something bad is happening, he knows his nightmare is coming true, but he knows he can do nothing.

"Onii-chan!!!!" Shinji suddenly starts screaming, banging on the window trying to get to his big brother. He is then yanked from that spot by his father as the glass breaks and again in horror watches as the AT Field begins to look like its bending, almost like it's trying to suck itself in.

And then suddenly it does, and with it a great empty darkness covers the entire area. Then slowly they all watch as the darkness begins to swallow Ill Gill and Kai into the empty void.

As this is happening Shinji continues screaming for his brother as he hears a voice in his mind, one that sounds so very different yet at the same time, Shinji could identify it as Kai's voice.

'I'm sorry Shin-chan, I'm sorry that I'm gonna leave you but don't cry, I promise that one day, I'll find a way back and then we can be together again. Tell mom and dad not to cry either and that it's not their fault, if it's anyone's fault, it's my own, I should've have checked all the possibilities. Remember, don't cry and be happy, tell mom and dad to continue Project E, that it'll still work. Well, this is goodbye for now Shin-chan, take care.'

With that, Ill Gill is completely swallowed by the darkness. Everything is back to normal as if nothing had happened, aside from the broken glass and the obvious disappearance of Ill Gill and it's pilot. Everything is silent except for the sobs of Yui and her son Shinji.
Japan 2015

Things are hectic at NERV, with the sudden appearance of the 12th Angel, and then the disappearance of Unit-01 as it was swallowed by an all too familiar black shadow, to some, now identified as a Sea of Dirac.

At the cemetery of Tokyo-3 a slightly aged man looks upon a grave he has not visited in almost 12 years. "Kai, it's been so long since I last came here. A great deal of things have been left unsaid, any with it a great deal of things has changed. Thanks to you, Project E was successful and we have been fighting and beating the Angels, but at this point I'm not sure if this is a good thing or bad. But, that's not why I came, in fact I'm not sure exactly why I came, the urge to come here after all these years is from today's events. The 12th Angel has appeared, and with it a Sea of Dirac, or rather the black shadow the swallowed you and caused your death. You might think this is none of your concern, but Unit-01 was swallowed by it and with it, it's pilot, the one you called brother, Shinji Ikari. Perhaps the reason I came here was to ask for your forgiveness, the one Yui told me you always wanted to be protected from Eva or the Angels, has been taken by the very things you wished to protect him from, a wish that I tried to take upon myself and do for your sake, a wish that I horribly failed at." With that the man, Sub-Commander of NERV, Kouzou Fuyutski left hoping that for Kai's sake that Shinji could be saved from the Angel.
In the white void of the Sea of Dirac, one Shinji Ikari, lies inside Unit-01 and it's entry plug, slowly awaiting his death, yet at the same time screaming for everyone he knows to help him, to save him.

Not far from Unit-01, something unseen watches, recently awakened from its long slumber by a familiar presence and then looks in slight confusion at Unit-01. 'Hmm....hmm... where am I..... is that an Eva.... Yes it's Unit-01. Was it sucked here as well but how?' The unseen 'creature' appears from the white void, something that has been forgotten and thought to have been destroyed 11 years ago. 'Shinji....... I can feel him...... he's in Unit-01..... he wants help... to get out.... Shin-chan...... what!? Yui...... she's there as well.....no.....it's different...... no it can't be!.... She's Unit-01?!?..... I see'

Inside the entry plug of Unit-01 Shinji feels a warm and familiar presence. "Mother?" and then a second presence not as close but just as warm, and before he blacks out he says two words. "Mother? Kai?"

'Shin-chan, I will protect you. I'll keep my promise. Let's get out Shin- chan. Lets get out together!!!!!'

Well, here's the Prologue for this fic, now to clarify a few things. The idea of Ill Gill came from the game Phantasy Star Online Ep 1&2, now no this will not be a Crossover Fic, I'm just using Ill Gill cause if my opinion he would make one badass eva/mecha thing. Another thing, about Ill Gill rejecting Kai yet still synching with him, since Evas technically have their own will, just can't really use them freely, I decided to do that with Ill Gill. I will be doing some interesting things with Ill Gill and Kai in this Fic in later chapters. Ah yes, one more thing if you didn't really understood or paid no attention to the summary(I suck at those), this is basically a AU-ish fic, which explores the possibilty of what could happen in Evangelion and how it would affect the characters and such, with the factors of Kai and Ill Gill tossed in the mix. Oh yes almost forgot, feel free to review, flame, constructive criticism, wutever, I could probably use it as this is my FIRST FanFic I've written, expect Chapter 1 to be on sometime next week or the week after as I still have to study for Finals(damn High School)