Neon Genesis Evangelion: From the Darkness

By DarkShadowX

Disclamer: I don't own ANYTHING in this fic except Kai, so leave me alone I've done nothing wrong, shoo shoo read the fic and be off with you!!

Chapter 1: Return of the Beast

Japan 2015, Tokyo-3

The 12th Angel is seen floating in the city, unaware of the attack that is soon to happen. Eva Units 00 and 02 are in position to use their AT Fields to neutralize the Angels Inverted AT Field. The 'rescue' operation, if it could really be called one in the first place; will be to bomb the Angel with all remaining N2-Mines, 992 mines to be exact, hopefully will destroy the Angel and, to put it in exact words, 'salvage Unit-01', it's pilots life is simply, irrelevant. But, this is not the attack to come the true attack will come from within the Angel itself.

"Units-00 and 02 in position, AT Fields at maximum."

"Mine drop commencing in T-minus 30 seconds"
Sensing the presence inside of Unit-01 become stronger, the unknown creature fully awakens and prepares to escape this void along with Unit-01 and Shinji.

'It's Time'

And suddenly, hell breaks through and the ground begins to shudder violently. The shadow on the ground, the Angel's true body, suddenly begins to break and all that is seen of the Angel's body is black and red.

"What the hell is this?" Unit-02's Pilot, Asuka, yells.

The sphere floating in the sky, the Angel's 'shadow', begins to contort and spasm. The white markings of the sphere vanish, what was once the shadow is now the Angel's body.

"What's happening?"

The techs checked their displays, one of them called out. "We don't know!"

"All of our meters and gauges are going of the scale!" said one of the techs, Maya Ibuki, as Dr Akagi glanced over at the readings

"But, we haven't done anything yet!" yells Dr. Ritsuko Akagi.

"Do you think it could be Shinji?" asks Major Misato Katsuragi, with an obvious tone of both, worry and hope.

"Impossible, Unit-01's power must be at 0!" retorts Dr. Akagi.

Then, the Angel begins to expand slightly as a spot of the Angel suddenly bursts, the Angel's red blood spraying out. A hand, soon accompanied by an arm, comes out and grabs a part of the opening it has made. Another hand is then seen grabbing the other part of the opening pulling it, widening the opening it has made making it appear in the eyes of some a twisted mockery of birth, as Unit-01 pulls itself out. Through the blood one can see the eyes of Unit-01 glowing with an unholy light, its' face hardly visible though as it is covered with blood. Unit-01 then begins to pull itself out using an intense amount of force and the unholy gleam in its eye shining brighter than before, it looks at its surroundings then at the Angel it is painfully killing, and then it's mouth opens and releases a howl of primal rage.

"Mein gott, is that what I'm piloting?" Asuka says, fear in her voice and a look of shock on her face.

"My god, what kind of monster have we made this from," Dr. Akagi questions herself, not noticing Misato looking at her from the corner of her eye. Continuing to watch a thought runs through Misato's mind, 'I know the Evas are copies of the First Angel, but what does NERV plan to do with them, what do they plan to do with them once all the Angels are destroyed.'

As everyone watches Unit-01 ready to seemingly about to burst the Angel from the inside out it stops, as if waiting for something. Then, the Angel again expands as once again in the same fashion as Unit-01, another what appears to be an Eva, comes out and then, from a non-existent mouth, along with Unit-01, release a primal howl, not one filled with rage but of victory, as if they have finally pinned their prey and are toying with it. The Angel, unable to take it anymore, explodes releasing Unit-01 and the other beast, as they come landing, the ground breaking and cracking around them from the impact, soon followed by a rain of red, the blood of the 12th Angel. Both beasts stand there seeming to bathe in the blood, and again release another howl. Unit-01 then proceeds to shut down and the entry plug is released. Everyone releases a sigh of relief, but then are cut short, as they see that the unknown beast, has yet to back down, standing over the entry plug as if protecting it, its red visor glowing with an intense, unholy light, is watching everything around it, daring anyone foolish enough to try to come and get the entry plug.

"Shutdown Units 00 and 02 and release the entry plugs", Major Katsuragi suddenly says.

"Ma'am, is that wise? I mean we have no idea what that machine is, we don't even know if it will attack us or not", a tech says, fear showing on his face and voice.

"Just follow my orders and shut the Evas down!" she yells, causing everyone, except Dr. Akagi, flinch in fear.

Reluctantly, the techs proceed to shutdown the Evas, the plugs released shortly afterwards. Both Pilots, Asuka Langley Soryu and Rei Ayanami, step out of the plugs but stay in their spots, their eyes never leaving the Eva-like machine that is standing a half mile away from them.

Watching the Evas shutdown, and sensing that there is no more danger, the beast then proceeds to return to its slumber, exhausted from breaking free. 'Take care Shin-chan, we shall speak soon, but not now, I must rest before I can come back.' With that everyone visibly relaxes and release the breaths they have been holding, as the beast shuts down, its red visor going black.
At NERV Headquarters, in the office of the Commander, Gendo Ikari, two men watch the events that have unfolded. One has a look of slight surprise and the other has a look of complete shock, as if he has just seen a ghost, or seen something come back to life.

"This..... certainly was.... Unexpected," Sub-Commander Fuyutski says after calming down slightly.

"Indeed, it seems 'He' has returned, but perhaps this can be of use to us. SEELE will be in an uproar at the events that have occurred," says the cold voice of Commander Ikari, not bothering to hide his amusement.

'And perhaps 'He' will be your downfall, he never truly did side with you, and with Yui gone, he'll most likely be hell-bent on protecting Shinji,' Fuyutski thinks as he watches the recovering teams heading to retrieve the Evas, their pilots and Ill Gil, the beast that has returned from the darkness.
"Shinji, Shinji, SHINJI are you all right!?" Misato yells, tears pouring from her eyes, and concern dripping from her voice.

Slowly, Shinji opens his eyes to see his guardian, as she gets within the entry plug and brings him into a tight hug, crying harder than before.

"I just... wanted to see everyone... one last time," he says, tired from his ordeal.

Before the realm of unconsciousness grips him, he hears the voice of his other roommate and fellow pilot say, "Aren't you going to punish him?"
NERV Headquarters

Back at NERV hours after what has transpired, Commander Ikari and Dr. Akagi are on the Umbilical Bridge of Unit-01's holding cage, standing before the beast as it is being washed, removing the blood stained on it.

"I've never seen the Eva look as terrifying as it did today. Are the Evas really on our side?" Dr. Akagi says, mostly to herself.

"Oh, sir, I think Major Katsuragi may suspect something," she says, this time to the Commander.

"Leave her be, for now," he answers, his eyes never leaving the face of Unit-01.

"Umm sir, just what was that machine we captured? It looks like an Eva, and the MAGI seems to recognize it, but there are no files pertaining to it," she speaks again, her curiosity getting the best of her, as she has the feeling that if the MAGI recognizes it, then he will as well.

Turning his gaze slightly in her direction he speaks in a slightly colder tone of voice, "it is simply a ghost from the past, it doesn't concern your attention, is that understood?"

Surprised at the tone of his voice as he gave the order, she nervously replies, "Yes sir."
In another Eva cage, the said machine sleeps, the blood finally washed off of it. As it sleeps a part of it awakens, checking its surroundings, looking for something. As it finds what it is looking for, it's visor glows a slight red as it generates its' AT Field, but low enough to be undetected by the MAGI.
NERV Hospital

Night has fallen, and all is silent in the hospital. No one is seen through out the halls except a nurse or two. While this is a hospital, it is exclusive to NERV personnel only, so there are no patients currently, but one.

In the room of Shinji Ikari, the pilot sleeps, his mind plagued by thoughts that he will be unaware of when he awakens. The only sound heard in the room is the sound of his breathing, indicating that he is very much alive and asleep, not unconscious.

The moonlight shines through the window, giving a ghostly glow to the room. The glowing becomes slightly brighter, but it is not from the moon. In the room there is an orange light begins to manifest and shape itself. The shape is in the form of a human male. The male is the thought to be dead Kai Shiatori, but if one were to look at him now they would notice the changes he has gone through and the changes he hasn't, as he seems to have been unaffected by the hands of time still looking like the 14 year-old he looked like on the day he 'died'. His hair is now a dark black, the brown color that once accompanied it is now gone, it is still shoulder length, and he has grown bangs that cover some of his face, some of his bangs are slightly spiked and those that are and a sliver-white color. He is still physically shaped the same, still wearing the black plug suit. But his hair isn't the only change, his eyes have now lost the black color, they are now a dark bluish-silver color and they appear to glow in the darkness and pale moonlight.

He approaches Shinji, as he then places his hand on Shinji's head. In that single touch, Kai sees everything that has transpired in Shinji's life. Emotions begin to run wild in Kai, but the strongest are those of sadness and hate. Sadness, for leaving Shinji and for everything he went through after Yui's death, and hate for that man, Gendo Ikari... no Rokubungi, for abandoning Shinji for 10 years only to have him come back to pilot that cursed creature known as Eva.

Wishing to relieve him of some of his sadness and the nightmares that are now plaguing Shinji, he uses his AT Field to probe Shinji's mind and force some of Shinji's few good, happy memories to the surface. Shinji now seems to calm down, and relaxes as he dreams, reliving some of his happy memories. Seeing that, Kai smiles and says, "Sleep well Shin-chan, soon I'll be strong enough to come back, then I'll help you fight the Angels, and to payback Rokubungi for all the pain he has caused you. You've lived such a hard life without mother and myself, I'll be back soon, but I can't tell you the truth about mother, I fear it would tear your already cracked soul apart. I hope I can help heal the wounds that have been inflicted on your soul, the darkness within yours is frightening, if it were to be released it would..."

A voice from his mind interrupts him, the same ominous voice that once frightened him but now seemed as a common thing, speaks. 'You must return, I can no longer hold back the MAGI, it shall detect us soon.'

With a sigh, he gives the affirmative. His body then begins to glow in the orange light of an AT Field, and then disappears from sight as if he was never in the room to begin with. Shinji stirs in his sleep, uttering one word, with a happiness that was once, for a long time gone from his voice, "onii-chan."
Back at the Eva cage that holds the beast, Ill Gill, it prepares to go back to its' slumber, but Kai still has one last order of business to take care of. He proceeds to once again use a small undetectable portion of its' AT Field, to enter the mind and soul of Unit-01.

In the realm of Unit-01's mind, the scenery is one of a park that used to exist in Tokyo-3. Sitting on a bench that rests under a tree and watching the scenery, the form of a young woman, perhaps in her mid-twenties to early thirties can be seen, dressed in a pink shirt, white lab coat and a black skirt, her short brown hair seems to sway to a non-existent wind, and finally her green eyes that hold so much emotion, but to one who can read emotions as well as Kai, he could clearly see all the sadness within them.

'Hello mother, it has been a long time hasn't it,' Kai speaks a bit nervous and hesitant to do so.

The woman, Yui Ikari, quickly turns her head in the direction of the voice. She looks at the boy with confusion etched on her face, but as she looks more closely, her eyes widen in shock as tears start to form and fall down her face. 'Oh my god, Kai, it's really you, son I've missed you so much. I thought you had died!' She embraces her son in a tight but warm hug, crying as she has seen the son she thought she lost years ago.

With some tears falling from his eyes, he returns the embrace. 'I've missed you too, but I'm alive and I'm right here. So much has gone on mother, but I know of what has happened in Shinji's life, and what Rokubungi has done to him'

Shocked that he knew these things, she asks, 'but how do you know, I mean yes it's true, but you haven't come in contact with Shinji in almost 12 years.'

'I visited him earlier; I saw what he has been through and how it has affected him. I plan on helping relieve Shinji of that pain but I will have to wait, I am still too weak to free myself just yet, but once I do Shin-chan will have his brother with him again and I can hopefully, remove the darkness that is hidden deep within his soul,' Kai says, knowing to an extent of what Shinji can be capable of if the darkness is free without anything to restrain it.

'I see I'm glad you're both well, but true I've sensed the darkness within him, but why do you seem so afraid of it Kai?'

Hesitantly, he speaks 'Shinji already has a powerful soul, but he is unaware of how to use the light of his soul, his AT Field. But, if the darkness of his soul would be free with no restraint and released within Unit-01, his AT Field will become dark, the light of his soul replaced by the darkness of it. The darkness he has could possibly and easily take control, filling him with the rage he has bottled up deeply within his soul. He would lose all sense of himself and others and just become a destroyer, with Unit-01 as his tool of destruction, and with the use of his AT Field it would most likely be impossible to stop him when that happens. That's why I need to be there for him, to remove the darkness or if no at least be able to act as a restraint for it.'

Yui is more than shocked at what she has been told. Questions flood her mind as she tries to sort them out. As she proceeds to ask on of the many questions she has, suddenly a second figure appears. The figure's appearance is exactly identical to Kai's however with one difference, his eyes are red. The figure looks at the two of them and speaks.

'Kai we must go, if you want to be free as soon as possible, then you will need to rest. I need to rest as well, I cannot hold the MAGI back any longer, it will detect us soon'

'Very well, mother I'm glad I got to see and speak with you again,' Kai proceeds to hug her again, as she hugs him back, 'I'll talk to you soon.' With that, Kai vanishes, leaving Yui and Kai's 'twin'. He then senses another presence within Unit-01, and smiles, he then begins to vanish but before he completely vanishes he speaks, but what he says is unheard by Yui, but is perfectly heard by the other presence. 'I see, so this is where your consciousness lies, interesting I hope we may speak soon, Lilith.'

The second presence, that of the Second Angel, Lilith, is shocked that she was detected by this unknown figure. But, before she can look more into this presence, he vanishes. No longer able to sense him, her thoughts are on him as there is something familiar about him, almost a nostalgic feeling.
Back in the inner workings of Ill Gill, Kai and his 'twin' are having a discussion of sorts.

'That wasn't wise, confirming Lilith's presence within Unit-01, she will start to try and figure us out and what 'your' purpose is when she remembers who you are.' Says Kai, slightly annoyed at his 'twin' for practically giving away his presence.

With a small smirk, the twin answers, 'perhaps, but you have to admit, it was certainly a surprise to find her there, since we know she exists there and must live in some sort of agreement with Yui, we may be able to get them to aid us.'

'Aid us? How?' Kai asks, now slightly confused at his counterpart.

'They may be able to help us, be free of this prison, but for now let us not worry about that, we will need rest for I believe Gendo will be trying to figure us out and what the purpose of our return is.'

Kai says nothing as he continues to look at his counterpart, wondering what he may be planning, and also how they had ever managed to agree with each other in the first place.

Sensing Kai's doubt, he gives a small chuckle and speaks, 'there is no need to worry as I have no hidden agenda in this, and if I did, it wouldn't be anything that will put you Lilim in any danger, you showed me after all that the Lilim deserve a chance at life.' It was true, Kai was a very interesting Lilim, for one as young as him, he had a great knowledge and amazing perception of things and the ways of life. His hatred for the Lilim had dwindled upon meeting this boy, now his hatred exists for very few Lilim, mainly those who are like that man, Gendo Rokubungi, does his hatred truly continue to live in.

Seeing the sincere look in his twins face and nothing but truth in his voice, Kai just nods his head, then vanishes as he has entered his state of rest, to regain the energy he has lost in this rather busy day. Soon, after the other figure, too vanishes entering his state of rest. Tomorrow, they will again try to contact those they believe can help, in hopes of freeing themselves before the 13th arrives.
Well, heres the OFFICIAL chapter 1 of this fic. I'm sure you can all pretty much guess what I've done to Kai, I had originally planned to do this in later chapters but my mind slipped away from me and I ended up putting it in this chapter. The idea of Lilith's conscious being inside of Unit-01 came to me from the fact that Unit-01 is a copy of Lilith rather, than Adam as the other Evas are, and since Unit-01 has a part of Lilith's soul, as does Rei, so technically they have a part Lilith herself, but I decided to mainly incorperate that in Unit-01. Now about Kai's 'twin' well I'm not gonna say anything about it, but your all welcome to guess and if you get it right, well you'll have to wait till later to find that out, but anyways have a cookie if you do. Now in the next chapter, I'll try to start focusing on everyone else, rather than just Kai and a bit of Shinji. Next chapter might be up by this weekend, oh and one more thing, if I go out of state during the summer expect no updates on this fic for about the two months of the summer, if not then I'll be updating pretty often.