Summary: Naruto, after the war is struggling to hold the Juubi that is sealed in him under his seal. So he decides to try something that Orochimaru gave him in his notes, something called a Philosopher stone.

After meeting the Truth he becomes an immortal and the unknowing first creator of Alchemy and Alkahestry. He decides to help keep balance in the world

Naruto x Olivier Mira Armstrong (No Harem)

Challenge from Noctus of the Thousand Blades.

Creator of Alchemy

Prologue

It had been five or so years after the war. The Bijuu were set free leaving him with the Juubi.

After he and Sasuke fought in the Valley of End the idiot reformed the Juubi from the halves of the Bijuu to try and control it.

It didn't go well as it killed him and went on a rampage. Naruto had barely enough time to seal it inside him with the help of Kurama. Through pure will power he was able to take out Kurama just as the Juubi went in.

He felt keeping Kurama locked up in him was unfair.

Thankfully he had learnt his mother's chakra chains on the Island Turtle as they seemed to hold it down long enough for him to seal it away. The Bijuu blessed him with halves of their power while keeping their soul outside him.

He even created a summoning realm for them to stay away from humans as they didn't trust anyone but him, hence the reason he was the only one who could even sign the contract.

He currently sat in a house in Uzushiogakure's ruins.

After the war the villages were a bit scared of him as he did have the Juubi inside him so he decided to be alone, hence the reason why he was in Uzushiogakure.

He decided to stay in the old village with the help of clones and rebuilt the main house in Uzushiogakure for him to stay in.

As he was rebuilding it he found out was where his mother grew up in before heading to Konoha. Apparently his mother was the daughter of the clan leader of all the Uzumaki.

Over the years he spent in Uzushiogakure he had been studying seals like crazy.

He groaned and laid back in his study room. He was constantly in pain, the Juubi constantly rampages against him inside him. Luckily the Bijuu's power helped keep him down.

Then he remembered some research that Orochimaru had given him, something that would steal the energy of something to create something else, more useful from it.

After the war Orochimaru had turned himself in and actually chose to help the village. Before his research was turned in the Sannin strangely gave him a large file, claiming "If anyone can achieve this it would be you kid. You were always the unpredictable one as young Sasuke use to say".

It was research on some old story called a Philosopher's Stone. It was powered by the souls of many of the few souls of the strong. Only downside was every single trial of Orochimaru's ended terribly as they died in a storm of red lightning.

It was Orochimaru's last stand on immortality and Naruto seriously thought he could actually do it with the Juubi as collateral though not for the immortality aspect but for the power it was theorized to have that it would steal from the Juubi to keep it from continuing to try and take over him.

He summoned an army of clones "Get to work drawing the diagram! I want it perfect with not a single symbol out of place!" He ordered as the clones nodded and got to work.

He sat in the center and started to gather Nature energy as he felt he needed to be strong for this. Orochimaru's notes said he needed to be ready for a lot of pain. The notes also said whatever or whoever used to make it would be bound by the stone.

"We are done boss!" One clone says as he finishes getting into Sage mode.

He opened his eyes and nodded "Let it rip!" He said as the clones sent chakra into the seal.

Naruto felt immense pain as the lightning of the seal started to tear him apart.

World of the Gate

He opened his eyes again to see a huge door with weird figures all around it.

The room was bright white with only the massive door filling the blank room

He went up to the door and touched it and instantly his mind was bombarded with images and memories. It was like he was getting memory feedback but from millions upon millions of clones. He gained so much knowledge of a material altering technique and much other things he never would have thought up. There were so many versions of it and so many ways of using it

He heard some laughing behind him making him turn around quickly to reveal a version of himself but made of a black outline. It reminded him of the Dark Naruto he had faced when he needed to gain access to Kurama's chakra but only pure light, no features were visible

"Oh well this is a happy surprise. Never thought anyone could have come here without losing everything. Many have been trying, mostly those sent by some man called Orochimaru" the shadow version said with a large smile.

"Hmm so the snake's notes were correct, who are you by the way?" he said as the version of him nodded.

"One name you might have for me is the World, or you might call me the Universe, or perhaps God, or perhaps the Truth. I am All and I am One. So this also means that I am You" it said as he pointed at him.

"Not the first time I've met a version of myself or someone who calls themselves God but if what you say is true then you have a feeling why I am here" Naruto said as the Truth nodded

"Yes though I am curious why you used human transmutation on yourself? You are perfectly healthy and I don't sense any dark intentions from you" the Truth asked as Naruto pointed to his gut.

"I have a powerful beast sealed in me that shaped the world long ago and that I fought in a recent war and it constantly fights me for control. Some days I have to wrap myself in my own chains to keep me from losing control. I thought maybe I could keep it weakened by making it power this Philosopher Stone" he said as Truth chuckled.

"And what would you do with this power? Revive a loved one, use it to kill others, rule a land, or maybe just flaunt it like you humans like to do?" Truth asked as Naruto frowned and shook his head.

"With this power I will live. No longer in fear of losing control of my body and releasing this beast back onto the world. I would never revive the dead as I believe the cycle of life is sacred. I believe life should never be taken unless it is to save the many. As for ruling a land I gave that up once I stored this beast in me and honestly I have given up the thought entirely. And I am not one to flaunt things like others, all I want is to live outside of the shadow of fear this things casts on me!" he yelled as the Truth smiled, showing a set of huge teeth

"The power you are seeking disrupts the balance" it said as Naruto nodded.

"I understand that but what if I were to use this power to keep balance. If there is more good than evil I will be the necessary evil to balance it, more evil than good then I will be the one that rids it" Naruto said as he rubbed his Sage markings.

"You really believe you can be that? Are you that arrogant in your abilities and cocky to think you can always help?" it said with a smirk

"Yes I do but I'm not cocky. You know all so tell me, is there one promise in my life I have ever broken" Naruto said as he held out his fist with a smirk.

The Truth smirked as he tapped his 'hand' against the boy's and smiled at the actions he saw of the boy.

'This boy is the perfect. So honest and near perfectly pure' the Truth thought as he nodded.

"Fine Naruto, you wish for the stone then we make a fair exchange. With the control of the Shinju you gain its eyes and some of its abilities disrupt the balance of life and death" it said as Naruto nodded.

"And you want me to relinquish control of them?" he asked as the Truth nodded.

"Naraka, Human, and Outer Paths as well as Izanagi and Izanami are the only ones I have problems with. Those that affect life, death and the souls of humans" it said as it held out his hand. "Plus you will be allowing me into your mind to help and the ability to use this new power you have seen from the Gate, the first ever one to use it, the starter of it all" it said as Naruto nodded.

"Then we have a deal" Naruto said as he shook the Truth's hand as the gate opened and he walked through it.

"Maybe you will be able to help truly keep balance of this world. We shall see young Uzumaki" he said as the gate closed.

Real World

Naruto slowly reformed himself in a storm of red lightning and stared at his body.

There was now a red smooth stone implanted in his chest right over his heart.

His energy felt strange and the stone was giving off the aura of the Juubi. He found the Juubi was still in his gut but it wasn't rampaging as the stone's energy was flowing from it.

"Damn that hurt but I have to thank the snake later" he said as he was hoping to train is his new abilities.

"We have a long time to train but for now let's just finish the details of our deal" Truth said as Naruto nodded

Chapter 1

-Several thousand years later-

A man frowned as he overlooked the city of Liore. He was dressed in a long tan trench coat with tan slacks, white button up shirt and black boots.

Strapped to his side was a wooden sheath with a dark red fur trim around the guard of the curved sword, which was shown by the curved sheath.

His spikey golden blonde hair had two spikey bangs that framed his face with three whisker marks on each cheek. His hair was held back in a ponytail as his vibrant blue eyes stared at sunset colored city

"So this is where the two boys are?" he asked as a familiar voice chuckled in his head.

"Yes it is Naruto, plus there are some vile things in this city" Truth said as Naruto nodded.

"So you just want me to follow the boys? Or go back to trying to find them?" he asked as he glared into the distance.

Naruto was referencing the first Homunculus, the one who killed the entire city Xerxes and started the one behind the war with Ishval. The thing actively tried searching for him many times to steal his power since it use to be in the Gate and knew of him and craved his power

He tried to save as many innocents as he could but Truth made him stay hidden as if the other Homunculi and their Father were to get ahold of him or know where he was it would ruin a lot of their plans.

Over his years he was essentially the founder of Alchemy, Alkahestry and other principles after chakra had died out with him being the last one to be able to use it.

But after the Xerxes incident, which he had been too slow to save the city from Alchemy became more widely used by everyone else.

He spent most of his time saving innocents from the actions of others. During the Ishvalan War that the Homunculi Envy started he used his skills as a ninja to help take innocent civilians and others out of the land to escape the Amestris army but he could only save so many people.

"Focus on the Elrics, where they go they will search for a stone and that will lead them to the abominations" Truth said as he nodded and stared down at the city as his left eye turned red and gained three concentric circles with nine tomoe, three on each circle.

It was the Rinne-Sharingan, or the Shinju eye as he liked to call it.

Rarely did he ever use his actual abilities from it rather than to help predict combat or memorize something. Occasionally he would use Tsukuyomi or Amaterasu but for the majority of his several thousand year long life he had never needed to use them much.

"I can sense a couple stones nearby. One is incredibly weak while the other two are those creatures" he said as a he could sense the stones through his own stone.

"Yes, but let us wait to see what they have planned. Blend in and try and get to the stone" Truth said as he nodded.

Over the thousands of years he and Truth's relationship was odd. At times the embodiment of the Gate was a strict boss, ordering him not to interfere and at other times he was relaxed and carefree, letting him save those he could.

But all in all the Truth was just and fair. Always keeping things balanced and Naruto didn't mind. Having its voice in his head was better than possibly losing control of the Juubi.

-Liore-

Naruto sighed as he drank some coffee in the church of the so called god named Leto.

He wasn't one to dismiss religion but when he knew the miracles of the so called god were nothing but alchemy used via a shoddy Philosopher Stone he knew it was false

"Hello, I'm sorry I didn't see you there good sir" a woman said as he looked over at her.

She had long brown hair with dark pink highlights. Her eyes were soft purple as she wore a plain white dress.

"It is fine, I am merely passing through and I am a bit interested in the religion of this town, that's all. My name is Naruto, what is yours?" he asked with a smile as her smile grew.

"My name is Rose, and if you have some time then I can tell you all about it if you want" she said as he chuckled until he heard a scoff in the back of the church.

"How can you believe such actions of this so called god? Pray to him and the dead will come back" the voice said as Naruto turned to see it was Edward Elric, one of the few people to use human transmutation and not lose everything, besides himself of course.

The Truth had told him of the Elric's try in reviving their dead mother and how Ed lost his right arm in it as Al lost everything and then the boy bound Al's soul onto a suit of armor in exchange for his left leg.

He hadn't met the boy personally but he did keep track of him and so far the boy came off a bit arrogant.

"Well to each their own, I always say. If this helps for someone have faith in something higher than us all then why try and crush it? Who are you to say what is real and what isn't?" he asked as Ed frowned and narrowed his eyes a bit.

"Do you really believe all that stuff about your so called god?" Ed asked, basically ignoring him.

"Of course I do" Rose said with a smile.

"35 liters of water, 25 kilograms of carbon, 4 liters of ammonia, 1.5 kilograms of lime, 800 grams of phosphorus, 250 grams of salt, 100 grams of saltpeter, 80 grams of sulfur, 7.5 grams of fluorine, 5 grams of iron, 3 grams of silicon and a little bit of 15 other elements" Ed listed as he closed a book.

"That is what makes up a single adult body, we know that with modern science but the reality there is no successful human transmutation has ever been reported. For hundreds of years scientists have researched it but none have been able to grasp it" Ed said as he stood up.

"Some say it is a wasted effort but I find it a lot more useful than just praying and waiting. Plus those ingredients could be picked up with the pocket money of a child, humans are incredibly cheap to make" he said with a smirk.

"I would suggest you be quiet boy, you have no right to crush the hopes and faith of others just because you don't believe the same that they do" Naruto said as he stood up and glared at him.

"Whatever, I'm an alchemist, a scientist so I just find it hard to believe in gods and things like that" he said as he walked out with the large suit of armor, his brother, following him.

"I am sorry for him, if you still have time you can still tell me about your church" he said as Rose recovered from having someone attack her faith and smiled.

"Sure, do you have a denomination?" she asked as he nodded.

"I do but I always like hearing of others and how many tend to overlap with similar teachings" he said as Rose nodded and started telling him everything.

'Why are you listening to her? You know her god is fake and the man Cornello is a fraud' Truth said as he mentally sighed.

'I know but just because of that doesn't mean I have to be rude to her and if anything it lets me stay here longer so I can maybe get a better sense of where those abominations are' he thought back as the Truth chuckled but stayed silent.

-Next Morning Tomorrow-

Naruto spent most of the day yesterday with Rose until the Elrics pulled her away with wanting to 'convert' but he let it slide since he wasn't to get involved, only observe.

As the morning started and the sun raised he frowned as he watched how things turned out and was a bit impressed how Ed revealed Cornello being a fake to everyone, essentially destroying the church and the stone from overuse since he couldn't feel the pitiful stone anymore.

'Do we go in to confront the Homunculi or do we just leave and follow the Elrics?' he asked as the Truth sighed.

"Leave, this portion of the land isn't our problem. We have bigger things to deal with than this" he said as Naruto sighed.

"Fine but I am not leaving Rose here without giving her a way to contact me" he said as he made his way through the rubble of the city.

"Why? She really serves no purpose even if she does join us" it said.

"Well she is broken and needs someone and to be honest I can't leave her like this, it's not who I am" he said as he walked into the town center to see people rioting and frowned as he saw Rose sitting at some diner with a blank look in her eyes

"How are you taking everything?" he asked as she looked up at him.

"Naruto?" she asked as he nodded. "Did you know everything was false?"

"Yes I did, but it is not my place to break someone's faith. Don't worry, I know you will recover from this" he said as she frowned.

"How? I lost the chance to bring my boyfriend back and everything I believed in was false!" she yelled as tears fell from her eyes.

"You do not mourn the death by making them return. You mourn them by remembering them for who they were. Life is sacred and should never be returned once it is lost but just because he is gone doesn't mean your life is over" he said as he pat her back.

"We are told a lot of lies in our lives but we always recover, I know you can when time passes" he said as he whistled and a black crow landed on his arm. "If you ever need me then just send a message tied to Kuro here and I will come back to you" he said as she looked at the crow that hoped onto the table and nuzzled against her.

She nodded softly as he pat her back again and started walking away.

"You just met the girl, why give her a way to contact us?" Truth asked as he shrugged his shoulders.

"She reminds me of someone from my past, a mix of Hinata and Sakura. It'd feel weird if I didn't offer her a way to contact me" Naruto said as he made his way out of town with a smile, disappearing in a flash of yellow.

-Base-

Naruto took off his coat as he appeared in his base in Central through his Hiraishin marker.

It was a sizeable house on the surface but underneath it had the same amount of rooms as an average mansion, which he was able to create with Mokuton. It was fully functioning with electricity, water and plumbing throughout it all as well as fresh air pipes. He used it to help those who couldn't live on their own, like Ishvalan refugees.

He turned as he heard his door open up to reveal a small girl as she ran up to him and jumped in his arms. "Brother!" she yelled as he held her and hugged her.

"How are you little one?" he said as a girl smiled at him as he carried her out of his room. She had dark tan skin with long silver hair done in braid as her red eyes were accented by her pale hair. She wore light pink shorts and a tan top with no shoes since they weren't needed in the house.

"What have I told you about going in my room?" he asked as she pouted.

"I saw the light and I was so excited for you to be home!" she said as she bounced in his arms.

He was often seen as a father or brother figure to the orphans and even to those with parents still. The elders saw him as an honorary Ishvalan and someone of their community because of how he was able to save them and take them from their war torn lands.

"Fine but next time wait for me to exit" he said as he set her down and she nodded.

Rayanne, the small girl who he was holding, was always by his side whenever he returned home. Her parents had died in the war and she was one of the few hundred or so that he had been able to save.

"Oh Naruto, good to see that you are back" an elder Ishvalan said as he entered the hallway with a smile.

"Yes, I will be back for a bit since I have things to get started on soon but I came to check up on everyone" he said as the man nodded.

He wore the traditional robes of an Ishvalan Cleric with a bushy white beard and short white hair.

"Everyone is peaceful as always, young Rayanne here was being a bit fussy as you were gone but beside that everyone is fine. Your associate is back and is waiting in your lab" he said as Naruto nodded.

"Thank you and look after Rayanne while I'm off" he said as he handed him the fussy eight year old girl.

"I'll be back soon so be good" he said to Rayanne as she pouted but nodded.

Naruto frowned as he walked to his lab. It was at the lowest level of the underground facility as he didn't want to disturb the others with the sounds of the machines.

"Oh good, your back. I thought I would have had to come back later" a male voice spoke out as Naruto turned and smiled at the man before him

"Miles, sorry for making you wait, I had some things to do." he said as the man took off his snow-blindness goggles to reveal his red eyes

He wore a winter version of the usual military outfit with his grey hair pulled back into a ponytail. He was of Ishvalan descent but was raised in Amestris long before the war began and was one of the few that he found to help him.

Miles was loyal to Amestris but also to his race and considering all that Naruto asked of him was info concerning a few things he allowed it.

"That is fine I have only been waiting a couple minutes" Miles said as he handed him a folder. "I was finally able to get everything you asked for"

"Thank you Miles, this helps a lot" he said as he flipped through the file.

"I still don't know why you wanted the list of deaths from Scar and some State Alchemists" Miles said with a frown as he looked around the lab.

"Because Scar is killing those in Central and even if some of these people are asses but the M.O of this Scar sounds a lot like Alkahestry, like my seals more likely" he said as he rolled up his right arm's sleeve to reveal tattoos on them. They went from his shoulder down to the first set of knuckled on his hands and palm of his hand.

"Wow that is some intense ink" Miles said as Naruto rolled his sleeve down and put back on his white glove.

"I need to find this man before he keeps killing, plus I am very interesting in his skills. The State Alchemist parts is because if Scar is going after them he would most likely go for those that are the most well-known" he said as Miles slid back on his goggles.

"I should be getting back, Major General Armstrong will be expecting me back soon" he said as Naruto nodded.

"Thank you again and don't forget if you ever need me just stab it down" Naruto said pointing to the knife at Miles' side.

He had given Miles a modified Hiraishin marker that was place inside the actual blade of the knife to hide the tag.

"I know and don't worry" Miles said as he waved it off and went back to the elevator and pressed a button as it closed.

Naruto sighed as he sat back in his office chair and flipped through the file. Normally he didn't involve himself with murderers but with someone who is so elusive and has killed so many alchemists interested him quite a bit.

Plus the fact that his Alkahestry was like the destruction half of his full arm piqued his interest in meeting the man

"Don't forget to focus on the task at hand Naruto. We need to figure out what their plans are. You foiled their plan last time just barely but this time it will be worse and much more complex" Truth said as Naruto nodded.

"Don't worry I have spies working to figure their plan out. I know of where a few of the Homunculi are and have close eyes on them" he said as he unstrapped his sword and set it on the desk with a sigh

"All I need is for them to make a move so I can get started with this" he said with a smirk as he popped his knuckles.

-Chapter End-

Okay so this is the introduction chapter of my new story ^^

Naruto will be doing his own thing for the most part, occasionally run into Ed and the others.

He has the Shinju's eye but rarely uses it, he has a much stronger version of Scar's arm, the Homunculi's healing ability and can use chakra and Alchemy with no seals.

I made Naruto look after the Ishvalan as I can see him trying to help them when the war began.

Also Father and the other know about Naruto since Father is a being that use to be part of the Gate and knew about Naruto when he passed through the gate. But Naruto is incredibly stealthy and can hide from Father easily

I added having the Truth in his head as a sort of "Boss/Ally" of Naruto since Naruto only did it to keep the Juubi under wraps and the Truth saw that Naruto could be useful in the future and someone who can be trusted with a Philosopher Stone (the first ever one as Orochimaru only theorized the stone and created the very very basics of Alchemy)

Also Naruto pre-dates Alchemy, Xerxes and everything else so he is older than Father and Hohenheim

I hoped you all liked it

Until Next Time

Rate and Review!

Buh-Bye!