Creation began on 02-02-18

Creation ended on 02-06-18

Neon Genesis Evangelion

The Living Alchemist

A/N: Inspired by what might've been just an error made in an earlier published information guide made years ago.

All he recalled before he lost consciousness was that he was cold. He never recalled any illuminated visions or obscured echoes from the past that he had no recollection of. Then, the next thing he did know, he was shown things beyond his sense of comprehension. Strands, waves, atoms, patches of hair and skin, places where life lingered and death ravaged, even signs of war and famine leaving their marks. It was as though a vast amount of information was being transferred from the universe into his mind against his will, overwhelming him.

What is this? He wondered, coming to, seeing a dark ceiling…and smelling the scent of blood and decay around him. Where am I?

"Are you alright?" He heard someone say, and saw someone else in a large suit of armor looking down at him. "Hello? Can you understand me?"

He slowly moved his head as he struggled to get up…and saw a boy, younger than he was, with golden-blond hair, laying the floor with a bloody stump where his left leg used to be…along with a gash of blood where his right arm used to be.

"Gah!" He gasped, getting up to his feet and comprehending where he was right now. "Where… How… Who…"

"Please," the guy in the armor spoke again. "I don't know if you can understand me, but please… Please, help him."

He pointed to the injured boy.

-x-

"…Who is he?" Winry Rockbell asked Alphonse Elric about the mysterious boy in the strange outfit as he sat away from them in the hallway.

"We don't know," the armor explained. "He just…showed up before I realized anything."

"How did you end up like this?"

"We were…just trying to bring her back."

The door opened and a small woman with graying hair walked out.

"Is Ed going to be alright?" Alphonse asked her.

"It's too soon to say for sure," she responded. "What were you two thinking, trying to bring your mother back to life? Nobody's ever succeeded in completing Human Transmutation and lived to tell about it. Something like this was bound to happen…and what's his story (she pointed to the unknown boy)?"

"We don't know who he is. He just…showed up in the aftermath. He doesn't seem to know what's going on, either."

"What is he wearing?" Winry wondered. "It looks like pajamas or unusual armor."

"Has anyone spoken to him?" The woman asked them.

"We're not sure if he even understands us," said Alphonse to her. "He seemed to understand that Ed was hurt, but after he got here, he just sat over there and hasn't said anything."

"Maybe he doesn't talk," suggested Winry.

"Or maybe he doesn't want to talk," suggested Alphonse.

"No," the woman stated in realization. "He's just confused. He was probably somewhere else before he ended up in your house and has no understanding of how he got there or why. So, he's disoriented by his current surroundings."

-x-

The ruins of the results of bombing the Twelfth Angel had the expected outcome, as suspected by Misato Katsuragi. The buildings within view were covered in the blood-like substance of the Angel's body, the shadow was gone, and Evangelion Unit-01 was destroyed beyond any reasonable doubt of repair. But that wasn't the worst part of the aftermath. No, the worst part that was the icebreaker was the ruins of the Entry Plug…and the mutilated remains of the Third Child, Shinji Ikari.

He screamed for help, thought Misato, looking down at his dismembered left arm on the ground, and we killed him…just to get rid of an Angel. We didn't even try to find an alternate solution that actually worked.

She was going to beat Ritsuko Akagi senseless when she got her hands on her.

Standing a few feet away, the Second Child, Asuka Langley Soryu, saw the remains of Shinji's legs laying a good distance from his right arm. She didn't really think he'd die from multiple explosions and a disabled AT-Field. Maybe a bump on the head and a concussion, but not this. There was literally nothing left of the boy.

Shiest, she thought.

-x-

It bothered him to see that who he had initially thought was a guy in a suit of armor was really nothing but an animated suit of armor when he asked for him to remove his helmet and face guard. He didn't have any prejudice or bias against any of them, but a suit of armor moving on its own and being possessed by a little boy after losing his whole body to an attempt to bring the dead back to life did leave him feeling that he had stumbled into a world unlike anything he did know.

Where am I? He wondered again, stopping in front of a calendar on the wall and seeing a large map and the date. "What the… Uh, excuse me?"

The woman known as Pinako, after redressing Edward's stump of a left leg, came over and responded, "Yes?"

"This calendar here, is the date accurate?" He asked her.

"Yes, it is," she answered him.

"Nineteen-Ten?"

"Is something wrong?"

How'd I go from being in Twenty-Fifteen to being elsewhere in Nineteen-Ten?

He banged his head against the wall and just wanted to believe that he was dreaming a crazy dream as a result of being sucked into the Twelfth Angel. Except nothing made sense right now. If he was dreaming, then even self-injury would cause him to wake up…and he was still here.

"Where exactly is here?" He asked her.

"You're in Resembool of the country of Amestris."

Resembool and Amestris, neither of which sounded Japanese at all to him…or relating to any geographic location he was familiar with knowing. Try as he might to think positive, there was nothing here that he could tie to. The world he knew was gone, along with the people he knew. His guardian was gone, his accursed obligation was gone, the father he detested was gone, even the depraved cause he tried to believe in was no more. He was somewhere else, with no ties or roots to bind him. He was…totally alone…and free.

-x-

"…Is there any chance of Unit-01 being repaired from this…incident?" Gendo Ikari asked Ritsuko the next day in his office, wanting to know the status of the purple Eva.

"Not at this time, sir," she answered, trying to ignore the shiner Misato gave her right eye for indirectly causing the death of the Third Child. "It has suffered extensive damage to eighty-two percent of its body and components. It'll be at least two months to fully repair the damage."

"And…what of the pilot?"

"The Third Child didn't survive. Fourth-degree burns and the obliteration of his body. We gathered what was left of him and sent the remains to the lab."

"Dismissed."

She left and was glad for to do so, leaving Gendo alone.

"The Evas pale in comparison to the Human Instrumentality Project, Ikari," he remembered SEELE 01 telling him during a previous meeting. "They may have similar regenerative abilities as the Angels, but even they have their limits if put under pressure with no time to adjust."

Unfortunately, he thought nothing of it so long as the Evas survived to continue doing their task, regardless of what became of the pilots. And as for the pilots, it was unlikely that they would be harmed to such an extent so long as the cores were intact, but this was unexpected. The usage of every remaining N² explosive against this Angel while negating its AT-Field had the unexpected backlash of negating Unit-01's AT-Field, leaving it vulnerable to the extreme heat and pressure of repeated explosions that even its armor couldn't protect it against.

"There's no one else that can pilot the Evas," he remembered telling Ritsuko after the Third Angel incident. "As long as they survive, that is what I'll have them do."

"With no regard to what they may want?" She had asked him, and he never answered back.

He didn't want to admit it at all, even to himself, but he should've just sent the boy away again. There wouldn't have been any reason to think about him beyond his former service to the Eva program…instead of having to deal with the possibility of putting the kid into the ground at a later time if he didn't survive.

-x-

Shinji returned to the Elric house. He wasn't sure why, but maybe if he did, he'd find some closure to what was going on right now. It seemed like a nice and happy home, full of something he barely knew of, even looking at several photographs of the family.

If they were so happy, why were they so sad? He wondered to himself as he set down the old photograph of when the family had their father involved in their lives, probably back when the brothers were still too young to recall many things.

"…Aaah…" He heard something down in the basement.

"Hello?" He called out.

"…Huurgh…" The noise came again, sounding like someone in pain.

Stepping onto the top steps leading down into the dark basement, Shinji had a bad feeling about what was down there. It was like something was reaching down his spine with an ice pick.

'My genesis… This is where it all begins…'

Slowly, he crept down the steps, wishing there was a light switch he could use to illuminate the shadows of this cellar-like chamber. Once he set his left foot on the floor, he felt something that didn't feel like a smooth surface. Looking down, he saw red smears around his feet…and his eyes widened in fright; he recognized blood when he saw it.

'The sky breaks… Light reaches for me… I'm awake for the first time… It's too late… I'm on the other side…'

Shinji approached the spot on the floor that was marked with a large circle that, for some reason, caused the hairs on the back of his neck to stand on end.

But…why does this worry me? He wondered. I've never seen it before.

"…Guuurgh!" The voice came…and Shinji felt something large and misshapen attack him from behind, sending him to the ground.

FLASH! He saw the Elric brothers perform their attempt to resurrect their mother and the horrifying repercussions that befell them.

'My genesis… This is where it all begins…'

He was in front of a large, double-sided door with those symbols he'd seen all the time in his father's office (not that he really cared about that), floating within a large, white expanse.

"Where am I?" He asked, but saw that he was alone.

Creak! The doors opened and he saw a large eyeball looking at him.

'This is where it all begins…'

The thing that attacked Shinji was as large as a person, but so misshapen that he couldn't call it a person. And the worst thing of it was that Shinji couldn't even find a face with which to attempt communication with the creature.

A homunculus, a failed attempt at Human Transmutation, he realized; he wasn't even sure how he knew of this, but was more concerned with just living to see the next day. If left alone in this agonizing state, you wouldn't be a danger to anyone, but you still cling to existence like a parasite in search of food.

Shinji kept the homunculus at bay with his arms, but its weight was still its great edge…and he could only keep it away from his body for so long. He removed his right arm from the homunculus and placed it on the floor…and then stabbed it with a kunai that formed from the material of the floor!

"Guh!" The homunculus gasped, and was then stabbed seven more times by Shinji with the kunai. "Gaah!"

A silence between the two of them lasted for a minute before the homunculus became limp and fell to the right of Shinji, right onto the Transmutation Circle.

"I'm sorry for what was done to you, but this is a better fate for you and the two that made you by mistake," Shinji told it, placing his hands on the floor in front of the circle, triggering its circulation of energy. To obtain, something of equal value must be lost, but in order to reclaim what was lost, one must give up what they obtained. If I send you back to whence you came, I undo what was done to the brothers.

As it struggled to get back up, the homunculus was suddenly breaking down.

"Huurgh!" It shrieked, its misshapen arms atomizing as its skin and exposed bones followed suit with them. "Aaaaurgh!"

Then, just as it completely atomized out of existence, Shinji lost consciousness and fell to the floor, hoping that by doing this, he had undone the fate that before Edward and Alphonse Elric.

-x-

Edward awoke to the next day, feeling like the events of what transpired the previous night were nothing more than a crazy dream. Strangely, though, he didn't feel any pain in his left leg or right arm.

"Hey, you're finally awake," he heard Winry say to him, and he turned his head to the right of the room where she sat beside him. "How do you feel?"

He raised his right arm to wipe the sweat off his forehead…and gasped at the sight of it!

"My arm!" He went.

"Yeah, about that," she uttered. "The boy that appeared at your house, Shinji, went back there for three hours, and then came back with Al's body when…he collapsed. Then, he just did something with his hands and some water and your hand was put back on your body."

"He…performed a transmutation and restored my arm…and returned with Al's body?"

"Yeah. He seems… He seems like he has a lot on his mind right now, and everything else is keeping him from properly adjusting to his current situation. At first, we thought he was going to try and leave the town, but then he came back. It might be that he has nowhere to really go."

Ed flexed his right hand for a bit. It felt like his arm had been restored, down to the very sensation, and then removed the blanket from his lower body, seeing, to his great surprise, his left leg had also been restored to him.

"Where is he now?" He asked her.

"Outside on the porch," she answered him.

-x-

The sunlight felt good on Shinji's face. It made him feel like a new person. And then, he looked down at the kunai in his left hand, pondering what to do.

"Hey, there," he heard someone say behind him.

He flinched and held the blade defensively in front of him as he turned to face them, seeing that it was only Edward.

"Oh," he responded, calming down and setting the blade on the porch stand. "How are you?"

"Good," he answered him. "About my arm and leg, and my brother's body… Thank you."

"You're welcome. Just don't do what you two did again, please. I've only been here for less than a day, but I know that Human Transmutation is something that only those, either desperate or curious, commit to keep from facing a difficult passage in their lives, and it's nearly impossible to achieve completely because you're reaching for the impossible that even the gods themselves won't do, no matter how much it's desired. And…even if it were possible, the price is still too high to pay for anyone."

"How'd you do it, though? How'd you get Al's body back?"

Shinji looked at the porch floor and stated, "You speak of this…Equivalent Exchange in the foundation of Alchemy, as though it were an absolute truth…so in order to obtain, something of equal value must be given up. The same applies to the reversal if applied properly."

"To reclaim what was lost, one must give up what they obtained," Ed realized. "You returned our failed attempt back to where it came from. When that happened…"

"It's basically undoing the price that was paid for unintentionally by you two. I'm sorry to say, though, it didn't undo what you did to keep your brother; the sacrifice of your arm was a different price you paid. But I somehow knew what could be done to remedy that lost. I just…did a transmutation and generated for you a new arm, exactly as the one you lost."

Ed held his right arm and thought that the regeneration of lost limbs was impossible, as no other alchemist had ever performed such an attempt. It didn't seem like it related to Human Transmutation, as he was still alive and never died.

"Still, it's impressive that you were able to survive such an extreme," said Shinji to him. "And you're, what, ten? Eleven?"

"Eleven. So…what will you do now?"

"That's the thing. I'm not sure what I should do. The life I had… Well, the life I once knew…doesn't exist for me, anymore. After last night…I sort of had an epiphany about why I ended up at your house."

"Yeah, about that… I just assumed that it was an unintentional result of the transmutation."

"No, your transmutation had nothing to do with my displacement here. I was killed where I was…at the same time you attempted the forbidden art. My soul just wandered between two worlds and ended up here. Maybe this body I have was made from your attempt to bring your mother back with the leftover materials used to create your homunculus, maybe my body just ended up getting transported here. Who knows for sure? There's no point in wracking my brain on trying to ascertain the 'how' or 'why' to my situation. All that matters now is…what I do with the time I have here."

"Still, it would've been nice if I saw her again. Just to see her smile once more."

"Yeah, it would've been."

-x-

What was the point of having a funeral when the father wouldn't have his son's remains buried underground like the traditional cultures required by law deemed? What was the point of a memorial service for the boy when there were no cremains to light an incense for? None of this made any sense to Asuka as she stood in front of the grave marker used for Shinji, three days after the small service he was given.

She was angry that only a handful of people came to attend, none of whom included his father. Only the two stooges, Hikari, the First Child, Misato, Kaji, the penguin, the three Bridge Bunnies and the sub-commander bothered to show up and say their peace about Shinji. Of course, she couldn't fault any of them just because they were the only ones that did; she just wished that more people would have shown up, that his father would've said something meaningful about him…that she herself had pulled him out of the shadow before it was too late.

"It should've been different," she said to the tombstone. "It should've been different."

-x-

"…He must've cleaned up the place," said Alphonse to Edward as they returned to their father's study, seeing no signs of their failed Human Transmutation.

"That explains why that State Alchemist that showed up yesterday didn't seem to find any indication of any taboos being committed here," Ed stated, picking up one of the books on the table. "He probably did it to make absolutely sure that we didn't get in trouble with the State Military in case they started looking around."

"This is probably where he transmuted that knife he had with him," Al suspected, looking down at the floor and seeing signs of transmutation. "Anything could've been transmuted here, though, so there's no way to be sure."

"Or he's a neat freak to a degree. He even cleaned the shelves."

Outside by the river, Shinji, pondering his situation that he only confided in with the Elrics and the Rockbells, swung his kunai around with no particular reason to do so. Not a fighter by any stretch of the word, but he figured it was better to be armed than defenseless against others if he was going to venture out into this world that he was part of. And…he didn't like the way that man, this Roy Mustang, looked at him, like he was being suspected of foul play or aiding and abetting suspected criminal activity. He was careful to leave no trace of the Elrics' failed attempt, and he covered his plugsuit with regular shorts and a shirt, but the way the guy looked at him, it reminded him too much of his father looking down on him.

"You seem very attached to that thing," he heard a woman say behind him, and turned to see Winry watching him.

"It's the first thing I ever transmuted," he explained to her. "I'll keep it for as long as possible. There's a lot about this place that I don't know. I should probably get out and explore it."

"You would likely find out whatever information you desire from the National Central Library in the capital city of Amestris."

"So Edward says, but to access the whole of information they don't release to the public, I would have to be someone else entirely. I would have to be something else entirely."

"Yeah, a State Alchemist. Is that really the path you want to take?"

Her question was out of concern, since there seemed to be nothing but bad history between the Rockbells and the State Military, but Shinji had his own reasons for needing more information.

"I honestly don't care much for any military organizations that are supposed to be tasked with protecting the people any more than any of you do," he confessed, "but what other alternatives do I have? Anyhow, I'm more of a pacifist. I doubt that I could anything that would go against my conscience and what I swore I wouldn't do again if I could live elsewhere without the bindings of my past."

"And what was that you swore you wouldn't do?"

"That I would never fight in any conflict I didn't believe in or knew anything about from every perspective. I was, more or less, duped into such a conflict by my father, and he seemed to know more than he let on…but never said more than what he chose to disclose. It doesn't matter, anymore, though. I'm a whole world…and over a whole century away from the life I used to lead. For the first time in my life, I have nobody to tell me what to do, leaving me in charge of making my own decisions."

"No parents, no home… Nothing."

"Nothing in life is ever easy. We simply try to make the best of it."

-x-

It was a crazy request from Pinako Rockbell, but only because she saw what he was capable of and knew of what he did to restore the Elrics. As he traveled down the path towards the nearest train station that would take him to Central City for the Alchemy Exam, Shinji had been asked by the elder woman to keep watch over the Elrics, since he was, technically, older than Ed and Al were by three and four years, respectively.

"Can I ask what you intend to specialize in if you manage to become a State Alchemist, Shinji?" Al asked him.

"If given the chance, alchemically-induced regeneration," he expressed.

"Medical Alchemy," Ed clarified.

"I don't want to fight against others, anymore. I want to do something that is the opposite of harm to others."

"But…Medical Alchemy has been considered a dead-end by most of the alchemic community."

But Shinji was hopeful in finding out what could be possible in that field. He had been gifted with knowledge without wanting it, knew how to perform Alchemy without ever seeing it be demonstrated to him, and he had the freedom to see it through to the end for as long as he was here in this world.

"What do you two intend to specialize in?" He asked them.

"Construction Alchemy," Al answered.

"Defense Alchemy," Ed stated.

"Well, then, best of luck to all three of us."

-x-

"…I heard Rei didn't show up for synchronization testing for the third time this week," said Hyuga to Maya in the NERV cafeteria, a month after the funeral for Shinji.

"No, and neither did Asuka for the second time," the young woman explained. "Section Two has them under surveillance, but neither chooses to answer their phones."

"What'd you expect?" Shigeru asked them as he walked past them with his empty food tray. "Someone they worked with was killed, and it was a serious blow to them. They believed the Evas were the safest place to be…and they were shown that no place is safe from multiple detonations of the highest sort. Over nine-hundred bombs and no AT-Field, the Eva's just a big target waiting to be dismembered."

"Some people are considering transferring out of Tokyo-3 after the last attack. If the Evas aren't a sound strategy against the Angels, then why build them?" Hyuga stated.

-x-

"…You authorized the operation to force-salvage the Eva, Ikari," went Fuyutsuki to Gendo in his office. "You ordered Dr. Akagi to retrieve the Eva by any means necessary."

"There was no time to consider every option, Fuyutsuki," he told him.

"There's always time to consider alternatives, Ikari. What point is there to not consider other options if we're going to do the one that ends up being the one that shouldn't have been committed? There's a lot of regret. A lot of anger."

"To defeat the Angels, I will do whatever I have to in order to ensure a future for humanity."

"Lately, I've had to reevaluate my belief in NERV's goals…and a young man getting killed instead of rescued by the paramilitary agency he got drafted into serving by his father is one of the many things I don't need to remind me that I'm guilty of the same depravity that most of NERV is responsible for."

"What exactly are you saying?"

"I quit."

-x-

"You hate trains?" Al asked Shinji as they were riding the train towards Central City.

"Oh, on the contrary," he responded to the younger boy, "I like the quietness of trains. You don't normally get this measure of quiet on a train. It's simple and relieves stress over time."

"You sound like you never had enough of any peace," suggested Ed to him.

"Yeah, too much quiet, never enough peace," he accepted. "Even in the darkest days of suffering, anyone can find slumber that allows for momentary peace, but for those that choose to inflict suffering onto others, their souls cannot know eternal rest. Ever."

"What?" The Elrics questioned, and Shinji had a look of momentary disorientation that quickly disappeared from him.

"Huh?" He reacted. "What'd I just say? Did I say something after not having enough peace?"

The brothers looked at one another before looking back at him and responded, "No, nothing."

Shinji turned to look out the window and felt some degree of detachment from his surroundings right now. He wondered if he had truly died where he used to reside? Had anyone managed to deal with the Angel? Did anyone think about him…or even miss him if he did die?

To be continued…

A/N: Here is the pilot chapter of another possibility to include in my multiverse storylines of Evangelion. It takes its inspiration from the original FMA anime, so be prepared for any eventualities where you encounter familiar faces of the past.