Chapter 1
Disclaimer: Neon Genesis Evangelion is owned by Gainax and My Little Pony: Friendship is Magic is owned by Hasbro.
"Interesting..."- Nightmare talking.
"Why me..." -Ordinary speaking
'And so it begins.' -Nightmare thoughts
'Aw hay.' -Ordinary thoughts
______________________________________________________________________
Drifting through the Aether, a being made of energy seethes in anger. Anger at being defeated by those below it's previous host so son after defeating the one who beat it originally. Anger at losing it's previous host... And most of all anger at itself for not reacting quicker and thus leading to it's defeat. Suddenly, it stops as it senses something. 'Hm... what is this now?' If a cloud of darkness could grin, it would as it senses a opportunity to possess a new body. One that it has the possible chance to shape to it's content. And in a flash, it crosses dimensions, a cackling laugh in it's wake...
____________________________________________________________
Gripping the empty plugsuit to her, Misato screams at the thing before her. "Give him back! GIVE ME BACK MY SHINJI!" A moment later a gurgling sound comes from Unit-01 and in a flash of purple light and a spray of LCL, it ejects a body which slams into Misato, knocking her to the floor. Shaking her head, Misato looks down. "Shin...ji?"
Two tired blue eyes with slit pupils look up at her as a small smile crosses a black furred muzzle. "Mi...sato-san..."
Up in an observation room, Gendo for once is completely speechless as his mind goes blank. Beside him, Fuyutsuki blinks before rubbing the back of his head. "I... take it that this wasn't part of the scenario?"
Closing his jaw, Gendo grunts. "No."
Inside Unit-01, Yui metaphorically blinks in surprise. 'That... was unexpected...' Then she mentally faceplams. 'Great... now everyone is going to think that I'm obsessed with unicorns...'
A few hours later finds Misato leaning back in the chair she's currently occupying, as she glares at her friend who's in a biohazard suit. "Is all this really necessary Rits?"
Looking from where she's looking over something on a computer screen, Ritsuko sighs. "Misato, Shinji was brought back as something not human, and yet intelligent. You were exposed to the LCL he was in so we're keeping watch on you both. We can't have something like... what happened happen to the rest of NERV."
Misato's scowl deepens as she gestures at the black winged unicorn staring off into nothing. "Look at him Rits! Does he really look like a danger?!"
Though the suit's faceplate, Ritsuko gives Misato a look. "Well, he did throw around those Section 2 agents like rag dolls somehow. And one of them is still in the hospital..."
Wincing, Misato shrugs. "Well, they did try to... er... attack him. And it's not like he was in a stable state of mind since he had just realized what had happened."
Ritsuko shakes her head until she looks at the screen and sighs in relief as she reaches up and pulls off her hood. "Okay, the results just came in and the Magi have confirmed that there's no biological agents we need to worry about."
Getting up, Misato bangs on the window catching the Section 2 agent's attention. "HEAR THAT MORONS!? THERE'S NOTHING TO WORRY ABOUT!" The two agents look at each other for a moment before they open the door, only for Misato to grab a key ring from one of them and go stomping back into the room. As she heads over to her transformed charge, however, her expression softens. "Shinji?" Since he doesn't look up, she sighs before unlocking the shackles around his legs. Gulping a little, she then hugs him around his neck. "It's going to be okay Shin-chan. I promise..."
__________________________________________________________
Standing in front of the drink machine, Misato slowly sighs as runs one hand down her face. 'Oh Shinji...' Suddenly two arms wrap around her causing her to scowl before her elbow shoots our and hits the person in the ribs causing them to let go. "Now is not the time Kaji."
The unshaven man slowly holds up his hands while gasping for breath. "Hey Misato, I was just thinking that with Shinji back, we should celebrate.
If anything, Misato's scowl grows. "Not interested Kaji."
She turns back and places some money in the machine before making her choices. Kaji just shrugs before giving her a grin. "Don't be like that Misato, after all with Shinji back, there's nothing to-"
He gets cutoff as Misato's arm shoots out and grabs him by the collar and slams him into the vending machine. Misato's rage filled face soon fills his entire field as view. "I will say this one last time you bastard. I. Am. Not. In. The. Mood." She soon stomps off leaving the confused Kaji before he places his hands in his pockets and follows out of sight. She soon enters the room where Shinji is still staring off into space, though his gaze is no longer so empty. Walking up, Misato swallows the lump in her throat as she gives her transformed charge a slightly shaky smile. "Hey Shinji." Holding out a can, she shows it to him. "Got you something to drink."
Without a thought, Shinji reaches out and takes the drink to Misato's surprise before opening it and drinking most of it in a single gulp. Setting it aside, Shinji turns and and sets it down and gives her a small smile. "Thanks Misato..." He trails off as he stares at the can as does Misato before reaching down and grasping it despite his hoof not reaching around it. "How...?"
Misato blinks before shaking her head. "Well... it's something I guess?"
Outside the observation window, Kaji's jaw drops before he looks around and leaves. "O-kay... maybe she does have a reason..."
After being transferred to one of the underground apartments deep inside the Geofront, Misato and Shinji are sitting at a table. Suddenly, Misato holds out a fork. "Here, try this."
Sighing while rolling his eyes, Shinji shakes his head. "Do we really have to do this Misato?"
She just gives him a grin. "Of course! It's for... er... Science!" She then begins nodding. "Yes. All this is in the name of science and discovery!" She then holds out the fork again. "Now, try holding this!"
Shinji just sweatdrops. 'No, this is all for your amusement...'
Sighing, he reaches out with a hoof and holds the fork in it without having to bend it. The fork somehow sticking to it. Misato just rubs her chin. "How the hell is it sticking when you can't climb walls..." She doesn't seem to notice the slight twitching of Shinji's eyebrow before she gets up with a grin. "Give me one second!"
She soon rushes off into the kitchen causing Shinji to lay his head against the table. "Now what is she after..." A moment later the twitch in his eyebrow is back in full force as Misato holds out a pickle jar. "You... want me to hold that too, right?"
Misato shakes her head. "Nope! I want you to open it." Seeing the deadpan look, she chuckles. "Well, you are still a male after all. So... opening jars is something you do."
Shinji's face feels like it's going to burn off as he remembers them checking that. Finally, he sighs and holds out a hoof. "Fine... give it here." Grasping the jar with one hoof, he uses the other to open it. "Ta-da."
Blinking at the slightly snarky tone, she shrugs as she grabs the fork and uses it to dig out a pickle. 'Stress maybe?' She's munching on it when she notices that his ears are rotating towards the door and he's looking at it. "Something the matter Shin-chan?"
Shinji looks at her in surprise. "You mean you can't hear Asuka or Rei?"
Her eyebrows raising, she turns towards the door and is about to answer when a Section 2 agent opens it. "Ma'am, the First and Second Child are wanting to see the Third."
Reaching over for a beer, Misato looks at Shinji now that she can hear Asuka lambasting the Section 2 agents outside in the hall with Rei's voice barely heard, though to the Major's surprise she too is demanding to see him causing her to smile. "Well, at this point Rits has confirmed that there's nothing infectious about you so..." She helplessly shrugs. "It's up to you if they can see you or not. This whole thing is classified to hell and back of course, but..." She sighs as she takes a drink of her beer. "You three would be cleared for it anyways since it's a 'Previously unknown risk of piloting Evangelion.'"
A small niggling feeling in the back of his mind tells Shinji that he should project a more regal bearing causing him to sit a little straighter. "Let them in."
As the Section 2 agent goes to do so, Misato blinks at the steel in her transformed charge's voice (she herself having about to get up and do so). The determination in it having altered the timbre of Shinji's new voice reminding her of the Emperor's voice when he made his last public appearance. She then leans back in her chair. 'Heh. Maybe this might turn out to be something of a good thing after all if we can change him back and he can keep his new attitude...'
A moment later after pushing aside the Section 2 agent, Asuka storms into the room with a superior look on her face. "Seems that that you made it again baka." She then snorts. "You would not believe the lies they were... telling... us..."
She trails off as her thoughts grind to a halt with the sight of the nervous looking winged unicorn sitting beside Misato. A moment later Misato places a hand on it's shoulder as it bites it's lip. "It... wasn't a lie Asuka..."
Rei then walks into the room and, upon seeing Shinji, nods unfazed by his current appearance. "It is good to see you okay Ikari-kun."
That snaps Asuka out of her daze. "WHAT DO YOU MEAN OKAY?! LOOK AT THAT!"
As Shinji flinches, Rei just gives Asuka an even stare. "Pilot Soryu, what is the matter? We were informed of the situation. It is still Ikari-kun."
Shinji gives her a thankful look and Misato is about to say something when Asuka explodes "THAT THING THERE IS NOT SHINJI! IT IS NOTHING MORE THEN A FREAK! A... A FREAK OF NATURE! A MON-"
She gets cut off as Rei takes a few steps over and slaps her. Asuka's head stays turned to the side as Rei glares at her with anger. "You will not speak of Ikari-kun in such a manner."
Seeing Shinji hanging his head, Rei turns to go to him and do... something as her instincts are telling her when Asuka grabs her shoulder and goes to spin her around. "How dare you-" Asuka suddenly finds herself being held a foot off the ground in a purplish field of energy. With wide eyes, both girls turn to see Shinji standing there with his horn glowing the same color and his wings flared to the sides giving him a quiet air of menace as he trembles with pent up emotions. "PUT ME DOWN RIGHT NOW YOU TH-"
Once more she finds herself cut off as Shinji speaks in a quiet, steely voice. "Leave Asuka."
Red in the face, Asuka starts shouting. "WHAT DID YOU JUST SAY TO ME!?"
Shinji just gives her even stare, his soft voice cutting through the air like a knife. "I've had it Asuka. I can deal with being called a pervert. A baka. And everything else. But... a monster?" He gives her a glare causing her to flinch. "Leave now before I do something that I'll regret."
He drops her and she falls to the floor shaking her head as she trembles. "N-no... you can't be the baka..."
Shinji just shakes his head. "I'm... still me Asuka. Just... different."
Asuka just keeps shaking her head. "NO! I refuse to believe that!"
Before anyone can say anything, she takes off past the Section 2 agents who had their hands on their firearms (and ignoring Misato's glares). A moment later once her footsteps fade, Shinji falls to his knees shaking as he begins to break down. "What... what am I? Was she..."
Totally lost, Rei looks over at Misato only to see the Major is not much different. Suddenly remembering a scene she saw outside school one day, Rei takes a few steps over and gets on her knees before wrapping her arms around Shinji's neck causing him to freeze. "It's okay Ikari-kun... I know that you're not a monster or a freak. You are Ikari-kun." To her surprise, Shinji leans into her as he fully breaks down. She just stays there holding him as he let's it out...
A few hours later finds both Misato and Ritsuko are inside Gendo's office. Watching the two women before his desk, Gendo takes a moment before speaking. “Dr. Akagi. Have you gained any further insight as to the Third Child’s… transformation?”
Clearing her throat, Ritsuko begins as she looks over some papers. “Well, Commander, the Third Child’s transformation into a Equine-“
She gets cutoff by Misato. “Winged Unicorn.”
Whipping her head around, the blond scientist glares at her friend. “What?”
Misato just gives her an innocent look. “Winged. Unicorn. That is after all what he is now.”
Ritsuko just takes a breath. “The Third Child’s transformation into a Equine.” She stops for a moment to shoot a short glare at Misato who smiles back. “Seems to be a complete one. Biologically, for all intents and purposes he’s no longer human. Though it seems his mitochondrial DNA and some of his human DNA still remains, but they’re genes that have nothing to do with appearance and we have no idea as to how long they’ll last.” Flipping to another page, she sighs. “His brainwaves are also… strange.”
Gendo’s reaction to this is to simply raise an eyebrow. “Is there any contamination that we need to be worried about.”
Misato clinches her fist while glaring at the man. ‘You are a fucking cold hearted bastard aren’t you!?’
Shaking her head, Ritsuko spares a glance at the Major before sighing. “No Commander. His DNA checks out as non-angelic in nature and more then that, he does not have a Blue Waveform Pattern emanating from him.” She then gestures at a screen showing some data. “We’re assuming that the changes in his brainwaves we’re observing are due to the changed structure of his brain. Almost a secondary mind, but that of a horse.” Running her hands through her hair, she takes a breath. “We humans are predators by nature. Horses and other Equines are prey animals. It’s to be expected that having both mindsets in the same body would produce odd brainwaves.” She then flips a page. “There’s several other physical changes we’re still figuring out. Such as the fact that his bones, while seemingly hollow, are also just as strong as if they were solid. Another being the high amount of Electromagnetism that is being produced inside his body.”
Fuyutsuki raises an eyebrow at this. “Could that be connected with his telekinetic abilities?”
Ritsuko just throws her hands into the air. “I don’t know! It’s possible but…” She grips the notepad in her hand hard enough for it to shake. “Everything about this situation is simply impossible!”
A moment later, Gendo speaks up. “Be that as it may. I expect a report on what happened immediately.”
Dr. Akagi just nods as she grimaces at the thought of all the work she’s going to have to do. “Yes Commander…
Gendo's expression doesn't change. "And also make sure to check as to whether the Third Child can still pilot Unit-01."
______________________________________________________________________________
The next morning as his eyelids begin fluttering, Shinji slowly comes to. ‘What…’ His eyes then widen before closing as he desperately fights not to cry as he remembers what had happened the night before with Asuka. “Damnit…” He stills as he feels a stirring against him before jerkily moving his wing up to reveal Rei curled into his side. ‘Er… when… wha…’ Feeling her snuggle deeper subconsciously, his wings suddenly snap wide open as he heavily blushes. A moment later he tries to bring them back flush against him, only to find they’re as stiff as a board. ‘Move damn you!’
He stills as he hears Rei’s voice. “Ikari-kun, is there a reason why your wings are stiff?”
Shinji rapidly tried to think of a way out as his mind races. “Um… I…”
Curious, Rei reaches up and runs a hand along the wing above her, a part of her mind marveling at how soft and warm it's feathers feel only for Shinji to twitch. A moment later she’s alone as the bathroom door slam causing her to blink. ‘Seems Ikari-kun’s speed has increased.’ Walking up, she knocks on the closed door before trying it and finding it is locked. ‘And seems that he can lock things as well.’ Hearing the sink on, she knocks again. “Ikari-kun, would you like me to bring you some food? I do not believe it to be a good idea for you to leave yet.”
Shinji’s trembling voice drifts out from behind the door. “Ye-yeah, that might be for the best. Thank you Ayanami.”
Rei just nods. “You are welcome Ikari-kun.”
Turning, she leaves, though she raises an eyebrow at the snoring Major spread out across the couch. Back in the bathroom, Shinji is looking at the running water with a sigh. “Just my luck…” After a moment of concentrating, his horn lights up helping him to splash his face (all of which he does instinctively). Upon finishing, he turns off the water and pulls a paper towel out of the nearby dispenser and uses it to dry his face while mumbling. "This is a nightmare..."
He suddenly stops as a silky voice makes itself know. "Hm... yes, in more ways then one." Looking around the washroom, Shinji gulps a little only for the voice to pop up again. "Oh, stop that you foal."
Licking his lips, he looks around again. "Who... who's there...?" He bites his lip for a moment. 'Oh Kami, please tell me that I'm not going crazy...'
The voice once more pops up. "No, you're not going crazy and enough of that."
Shinji blinks as his eye catches something and he looks back at the mirror to see his scowling vestige. "What the..."
The image of him (with a more feminine look he notes) smirks. "Now then... since we're going to be sharing this body..." The image rolls its eyes with a long suffering sigh. "No, I'm not one of these 'Angels' that you're so worried about foal. Now then... it's time to explain some things..."
__________________________________________________________________
Walking into the cafeteria, Rei walks towards the breakfast selection before looking them over. 'Now, what can Ikari-kun eat...' Looking over the meat and then eggs, she walks to the cereals cocks her head to the side. 'Can horses eat cereal?' Pondering this for a while she reaches over and grabs some bran. She also grabs a muffin for herself and some fruit salad for Shinji as well as a small container of Miso for Misato. Paying for it and some drinks, she walks back towards Shinji's room, deep in thought as to her recent actions.
'Why am I acting different towards Ikari-kun?' Frowning, she looks up. 'He is the same person. Is it because he looks different?' She suddenly stops as a confused expression crosses over her face. 'He is different. He is now unlike the others... like me.' Blinking at the strange thought, she starts walking once more. 'He is not human, like me.'
'His original body was lost and now he is in a new one... like me.'
'He is... unique. Like me.'
'He is... like me? Yes.'
She thinks back to the night before and feels a flash of anger towards the Second Child. 'She... hurt him. Does she see him like me? As something not a person?' At that thought, a even bigger flash of anger rushes through her before being supressed. She then remembers how she felt when she saw him break down. 'My heart... it hurt? Why? Was it because... I failed to protect Ikari-kun and thus he has had this happen?'
'Yes, I failed.'
Her eyes narrow in determination as she strides past several NERV personal. 'Never again. I will not fail Ikari-kun again. I will protect him.'
Her facial expression blanking as she passes the Section Two guards, she walks in and notices Shinji looking at her in surprise. He trots over. "Here, let me help Ayanami." Before she can say anything, his horn glows some as do the objects in her arms before they float out of them and are placed on the table. "There we go." Noticing the expression on Rei's face, he blinks some. "Um..."
Rei just walks over and looks at the objects on the table curiously before blinking and looking at Shinji. "A most useful ability."
Her eyebrows raise as Shinji grimaces and lifts a hoof to look at it. "Well, I suppose that I should have gotten something useful from this..."
Rei just reaches over and lays a hand on his shoulder causing him to look at her as she gives him a kind look. 'He is like me. Different from the others. Alone. Unique. I will help you Ikari-kun...'
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Haven't seen this for month's, done with planning it out on spacebattles?
871748
For now. Still working on it but putting together the next two chapters.
This... this has potential
It will interesting to see how well you draw that potential out. 
...Holy crap dude. Between this and the Harry Potter cross, you've caused me to LIKE Nightmare Moon. It's like the Loki Redemption fics that came out after Avengers was released. If done right, you can like the villain.
Hm... Very interesting. Is his color scheme more akin to Nightmare Moon or Luna?
I have only one nitpick with this, and that's... Rei's sudden overprotectiveness in relation to canon. Still, it's your story, and thus whatever happens is up to you. Also read that HP fic on FF.net. Liked that one so much.
And with a faving, I say unto thee: "THE FUN HAS BEEN DOUBLED!"
871865
His coloring is basically Nightmare's with his normal brown hair as a mane.
871874
Ah... that somehow makes me laugh.
And the award for most awkward moment goes to Shinji getting a wingboner from sleeping with Rei.
871912
Oh... it's pretty funny. Of course... some might take his looks the wrong way...
871960
Not sure I get what you mean on that...
Ok, pump the brakes here. There is a major flaw in your description, you failed to specify whether your crossing over with the manga or the anime!
871983
He looks like a male Nightmare Moon, now who might have some issues with his appearence at first...
872521
I'm going with the original anime.
872560
Ah, I see. Makes sense.
872560 Excellent! TO THE REFRESHER CAVE ROBIN, AWAY!!
871957
It's not Shinji without him getting uncomfortable...
872570
*Grins widely*
Quick question that didn't come up on Spacebattle, does Shinji being 'reformated' with NMM's appearance include getting her cutie mark? Or are you saving one coming in to give Ritsuko fresh fits?
Bonus points if it coming in is captured on video.
872685
Going to wait to give him one. Just to see Ritsuko once more lose it.
872704
Using your author powers to torture Rits for our amusement?
mylittlefacewhen.com/media/f/img/mlfw5118-da.png
872774
This is me that we're talking about after all.
I'm following this on Spacebattles but I'm just lurking there so let me tell you here that I absolutely love this story.
872882
Cool!
Decided on a whim to read this when I saw it in the latest stories list. Get as far as the key to thoughts and speech thinking they are done in a fairly familiar way, check the author's other works only to find a very familar HP/MLP cross I had been tracking for some time on FFnet. This discovery has led me to have some fairly high expectations for the story, and if the first chapter is any indication they will more then sufficiently met.
after reading this i can say only this.......
PONY SHINJI IS BEST SHINJI!
Nice to see this gathered together, I think this copy needs a divider after Yui's thought. It seems to be the only scene change that doesn't have one. It might be nice to have a better description of the lab (cell?) that Shinji's being held/staying in.
876637
If you're talking about the lab where Rits was examining him after he returned, then it's the normal medical lab shown in the series/in Real Life. As for where he's currently staying, it's just a one room apartment with the bedroom, kitchen, and living room all sharing the same space. He gets no privacy outside the bathroom (and even there considering that this is NERV...).
876685
I figured it would be simple (and for some reason I was under the impression he was shackled to something), but all my knowledge bar a few clips comes from fanfiction : )
876896
Ah, the only shackles there were was at the very beginning and that was his legs shacked together to prevent him from running.
I saw a really cute pic of Luna and Shinji on Deviantart awhile ago, and considering their similarities in personalities i figured it was just a question of time before a fic about the two of them were written, but i have to be honest, i never expected it to be written like this.
894023
I've seen that pic too and it was part of the inspiration for this. And how did you expect it to be written?
Well, something with Luna getting to earth, kinda like your HP/MLP fic or Shinji getting to equestria.
900574
Who said anything about him not going to Equestria at some point?
I meant in human form, Shinji transforminf into a Alicorn was something i did not see comming.
This chapter was very choppy. It seemed entire scenes would go by in a few sentences and so many details were lost it was a tad difficult to follow. But I'm going to put a little faith in the author of the first FIM fiction I've ever read, (Wizard and Lonely Princess), and see how this all plays out. I like the premise, and surprisingly enough, nobody was too ooc.
Rei sympathizing and protecting a non human? Yeah I can see it happening.
Didn't really care for the ending as well as a bit of the anime (dramadramadramadramadramadramadramadramadramadramaF*ING DRAMA!), but overall it was good. So yes, this has caught my interest, specially with Nightmare Moon.
I'd also like it to be known that I've ALWAYS despised Asuka.
Because reasons. Why are you not in the fucking robot yet?
...sorry, I had to.
Pilot robot. Become pony. Get girl
Buck everything else.
I somehow feel like everyone is overreacting to everything this chapter, and usually the wrong overreaction.
)
Gendo showing surprise? Gendo doesn't show surprise. It's his thing. He could witness the Loony Toons themselves rocket though NERV and smugly say "Just as planned." He might be surprised, but he'd never show it.
Asukra hating on Shinji straight away? I would have thought that fear would come first, given it's "A previously unknown risk of piloting EVA".
Shinji counter-hating? That feels like the wrong reaction for Shinji (I mustn't run away) Nighmare Moon (You call me a monster?! TASTE THE POWER OF THE NIGHT!) and even a random pony (W-why would you call me something so mean?
And Nighmare Moon being a head voice? Why wouldn't she just lurk until the time is right, then go 'Assuming direct control!'?
Welp, shit. I was just going to go up the stories list and read the Wizard and the Lonely Princess stories in order, but damn. One chapter and I'm hooked. Guess I'll see everyone else at the end of this 60k plus ride...
We need fan arts rite nau!
5322292 OMFG, your picture
best dad of the year