A week later the city of Tokyo three was going through changes the fliers made of changed by Seele where in the air manipulating clouds to make it snow to give the city it's first true winter.

People where in winter coats for once seemingly enjoying it.

In Nerv Misato was walking With Shinji she looked down at her feet making sure she didn't trip over her four legs " Ok now is the next one leg two of three? How do you keep track of all this legs?" she said puzzled.

Shinji chuckled to himself, "stop fighting it and go with the instincts Misato! It's how I was able to fly!" he said taking to the air for a moment before landing.

Misato rolled her eyes and then struggled to turn a door knob with her hooves only for Shinji to stop her and point to his horn.

Misato face hooved and her horn glow red making the door knob turn letting her in as she said, "Don't you tell anyone about this!"

Shinji chuckled to himself, "Why would it? This is a military base Cameras are watching us at every moment!"

Misato's eyes widen as she realized she was on Camera and said, "Oh buck me!"

shinji blushed for a moment before Misato gasped and said, "That's not what I meant!.. I mean don't get me wrong, you're hot.. I mean that is to say..OH HORSEAPPLES!" She said screaming in rage as she stomped the floor for a moment.

Shinji was red in the face and had a smirk as he giggled, "So you think I'm hot?" He then flipped his mane and put on a smirk that had a shine come form his teeth.

Misato was red and looked down, "now I'm being teased!"

Shinji then trotted into the door to see Maya who was petting a sleeping Bat pony Colt who had grey fur and white mane and tail.

Maya smiled and said, "Nice of you two to make it, Anyway we are getting a back up pilot who was changed by seele so made him feel welcome. As it is he is just back up!"

Shinji nodded and said, "Come along Misato!" he then turned and trotted off.

Misato then looked at her hooves and said, "Wait shinji how do I turn!?" she called out in a panic.

She was then covered n Shinji's magic who hovered her turned her around and set her down and then trotted out, "that was embarrassing!"

Later on at the hanger the new Pilot trotted in a grey furred Pegasus he then bowed" Hi I'm Kaworu Nagisa" he then got close up to Shinji and smiled and said, "And what's your name Tall purple and handsome?"

Shinji backed up and said, "Shinji and I I'm flattered but that's not my thing!" he said sounding kind of embarrassed.

Kaworu then winked and said, "How do you know unless you've tried cuddling with a colt?"

Misato blinked before blushing and pulling Shinji close, "While we accept all forms of love in this base, we still have harassment laws Buddy! He said no, now move on."

Kaworu looked saddened, "ok then.. But do you have any idea how hot he is?"

Misato then point at him with a hoof and said, " yes I bucking do!"

Shinji was red under his fur to the point he was starting to look like an alicorn version of Big mac.

Later on in a sink Test Kaworu was In the plug for unit-01.

Maya now had her little Bat pony Colt on her shoulder as she looked at the results, "he's sinking slightly higher then Asuka, and the weird part is we forgot to reset the Eva for him it's still set to Shinji! Maybe it has to do with the fact it's S2 engine is the only thing powering it? Making it so it's not picky with a pilot."

The little bat pony just chippered and start hanging form Maya's arm by his tail so he was upside down.

Maya looked at him, "Chester What did mama say about hanging off of people?"

Chester then blinked and said, "Ask first?"

Misato then hovered a cup of tea to her mouth with her magic as she said, "Maya an adopted mother how cute! Now on the subject of Ponies and parents where is Shinji's mama lun.. I mean Yui!" she said quickly back spacing her slip, as she took another sip form her drink.

Makoto looked at the results and said, "Something about Rei should be alone while she has a cold or something motherly like that!" he clearly wasn't focusing on it.

Shinji raised and eye brow as he watch Kaworu come out of the Plug his fur seemingly dry ad he said, "Wait I have to use magic to keep myself dry.. Something weirds coming on here, or I'm not an alicorn!"

Misato nodded and whispered, "I'm with you he is creepily cheerful like the anti-rei.. wait you don't think?"

shinji whispered "Seele? Well one way to check." He then hovered a phone out of his saddle bag and hovered out it's pen and he used it to send a text to rei's phone, "show mom this message we got a weird stallion need her to check him out in a dreamy way!" he then hit send.

Later that night as Kaworu slept he was dreaming about moving to Lilith ready to touch it as his core shined inside of his body.

When he froze to See Luna walking in and she said, "Thou truly are an angel in pony flesh!"

Kaworu blinked and said, "Second hand Pony flesh a seele gave his life up to put me in to this body." He said that emotionlessly.

Luan rolled her eyes as she said, "Are all angel as mad as thou? Or are you just special?"

Kaworu smirked and with a smile said, "We where here first, the Lilin where a mistake of another life seed landing on the same planet. Mistakes most be correct. I thank Seele for doing so, But we've never seen life forms like you! As such we'll allow you to remain for study!"

Luna growled as she trotted to the frozen Angel and touched his chest and said, "the only goodness in that was another seele died how ever when you awaken your S2 engine will be active all will know what you are! You lose!"

At that moment Kaworu awaken his chest glowing making him run off and take to the air as he flow form the room on base through the halls as the humans try to fire on him only to summon his A.t field as he fell to the Lilith room.

Only to gasp in shock when he got there to see no Lilith but Unit-04 Who quickly grabbed him as Toji smirked.

The pilot then proudly said, "We destroyed her along time ago and kept it secret. keeping a unit and pilot in this room in case someone tried to get her, to reveal Seeles!" he then crushed the angel in the Eva's hands.

Later on That night.

Shinji was at the harbor sailing out a paper boat with a picture on it, "farewell you fool I'm only doing this because you talked and tried to reason and make peace with something that calls this place home, you are proof just maybe maybe it would be possible for peace to have happened if not for Seele messing with your heads!"

The male Alicorn then spread his wings and flow off.

When he made it to Misato's apartment he opened the door and as soon as it was closed Misato tackled him.

Shinji's eyes widen as Misato's muzzle was on his muzzle it wasn't a kiss but it was close and Misato said, "Shinji I honestly can't fight this feels anymore!" She then truly kissed him.

Shinji's wings flared as his eyes widen and his horn sparkled in little hearts made form his magic.

The hearts being made form magic was happening to Misato as well, and in a moment Shinji closed his eyes and returned the kiss.

Elsewhere

The last three Seeles were meeting in person dressed black suits and the mask seele mask, they were in what looked like a dark basement with a white table and chairs.

Seele one said, "So all other plans failed manual destruction of the now ascendant is the only option left!"

Seele two clapped as he said, "Sadly so!"

Seele three sighed, "we most ready the mass production models!" They all three then got up and left the meeting room

To be continued

And to the guest reviewer I didn't even hear about that other story till a few weeks after this story was post so the similarities at the start are just a coincidence, and as a lot of stories start off with something goes wrong when Shinji is absorbed by the Eva, it's a cliché coincidence at that. now as the story is on it's final leg please calm down and just enjoy the ride.