AN: I know it's been done already but I decided I'd give it a try too
Chapter one:
The streets of Konoha were all quiet, except for one where there appeared to be a a small child with blonde hair and blue eyes running away from other villagers. This was Naruto Uzumaki, the unknowing jinchuuriki of the Kyuubi no Kitsune. Today was October Tenth, better known as the 'fox hunt'.
As he was running, he didn't notice the other person in the street. He ran straight into him and before he could get away he had a hand over his mouth and was dragged into a ally. The person who grabbed him quickly said "I'm not going to hurt you, stay calm okay?" Naruto nodded and the man let him go. Naruto quickly examined the man before him, he looked to be 5"11 and wore a brown cloak. Inside the hood there appeared to be blonde hair. The man then said "What is your name? How old are you? Why are they after you?" Naruto was afraud the man would go away when he knew who he was but sighed and said "Naruto Uzumaki, I'm five today and I don't know why everyone hates me."
The man appeared to be thinking for a moment before saying "My name is Ed, do you want to learn something super cool? There should be no one else able to do this around here." Naruto gaped at the man. He wanted to teach him something even Hokage-jiji can't do? "Yeah okay, let's get to my apartment. I need to learn fast!"
Upon arriving at the apartment Ed was disgusted. No five year old should live alone, let alone in a place like this. He quickly decided to go get some proper food and furniture tomorrow. He pulled out a scroll and said "All the stuff we need is in here, to do this you need a lot of basic knowledge okay Naruto?" Naruto nearly cringed on finding out he needed the knowledge but if this gets him a super cool skill it's worth it. He quickly nodded and Ed stateach unsealing the learning material.
-Timeskip: One Month-
In the month Ed had been staying with Naruto, Naruto had learnt quite a lot about the history, geography, biology etc. about the elemental nations. One day he was studying when Ed came over and said "Naruto, it's time for you to learn alchemy. I can't do it first to show you so this may be difficult." Naruto just nodded and listened to the explanation coming. "To do alchemy, there are basic things to remember. You must use a thing called a 'transmutation circle'. You must also remember the main rule, "Equivalent Exchange". This means you can't just create things like gold from thin air." Naruto nodded vigorously.
-Timeskip: Four Months-
Today Naruto was practising drawing a transmutation circle in hopes of learning to draw one fast enough to be combat ready. As he finished the circle Ed came over and said "It's time we train your body too, Once you get some muscle, I can teach you how to fight." Naruto just started cheering. Fighting means he's getting closer to being a ninja!
-Timeskip: Five Months-
Naruto was walking back to his apartment for another alchemy lesson when he heard a lot of yelling. He decided to go see what was going on. When he got there he heard things like "We haven't had the demon chase in so long!" and "The demon needs to die!" He was about to start running away but was discovered. As they all started chasing him he sprinted back too his apartment. Once in there he placed his hands on a pre-drawn transmutation circle in order to make a wall of earth come in front of the door.
He quickly ran over too Ed and said "Ed! Villager attack, they saw me and are on their way!" Ed just nodded and grabbed Naruto. He then put him in his bedroom and shut the door. Naruto quickly started trying to draw a transmutation circle in case they get in. While in the room he could hear a lot of shouts.
While Naruto was in the bedroom Ed was quickly sealing all the supplies for lessons and writing a note on top of the scroll. After that he stood waiting for a few moments until there was a explosion and dust filled the room. Once cleared he could easily see the mob of people, civilian and ninja. It was also obvious who the leaders of this was. One was a Hyuuga, wearing a standard Chuunin uniform. Another was most likely a Yamanaka considering his Blonde hair is the same shade as all the others. The third leader of this small mob appeared to be a normal Chuunin. From the looks of things there were 15 ninja in this group, 10 Chuunin and five older Genin.
The Hyuuga leader quickly said "Give us the demon brat and we might let you live." Ed just sighed and said "Your not getting the boy. His burden is enough." Ed quickly got into a fighting stance to be prepared. Soon enough the mob tried to charge, but Ed quickly dispatched them. Soon enough though, Ed was overpowered due to numbers and knocked unconcious before they kept attacking him. Eventually it seemed obvious Ed had died. They all cheered and then went to go after the 'demon brat' but found this door was blocked with a lot more earth so the ninja quickly went through more hand signs and called out their jutsu's. There was a small explosion and once the smoke cleared they found a empty room with a window open.
Naruto quickly charged down the street towards the Hokage tower. He could hear the mob coming so he tried too speed up but then tripped. He was about to get up before he felt a blow to the back of his head and fell unconcious.
When Naruto woke up he found himself in the hospital. Once he sat up he heard a kind old voice say "Good morning Naruto-kun, how are you feeling?" He turned his head to see the Hokage sitting there. "Good, thanks Hokage-jiji, I take it I got beat up again?" The Hokage just sighed and said "I'm afraid so Naruto-kun, you must forgive the villagers, they will accept you eventually, I don't know why they don't already." Naruto replied "I'll prove to them I'm not the Kyuubi someday don't worry." The Hokage was stunned into silence until he said "You know of the Kyuubi? How?" Naruto went on to explain how he found out:
-Flashback-
Naruto was currently going through his physical training until Ed came over and said "Naruto, I found out why everyone hates you. I don't think your ready to know yet but I can tell you if you want." Naruto wins tangly replied "Please tell me! I must know." Ed quickly explained that Naruto had the Kyuubi in him but wasn't the demon itself. He waited for Naruto's reaction until he heard "Okay. I trust you so I know it's true." Ed just sighed in relief and let Naruto train.
-Flashback End-
Naruto then said "After that, when I finished training he had talked about it since he thought I was hiding my feelings on it, I understand perfectly." The Hokage then said "And who is this Ed? I'd like to meet him." Naruto just said "He's my sensei. I last saw him in my house before he put me in my bedroom to hide from the mob." The Hokage paled slightly. There were a few deaths in this mob, all accounted for, except one. This must be that 'Ed'. The Hokage then said "Naruto, I have to explain something to you..."
After explaining what happened to Ed the Hokage noticed Naruto just went quiet and said nothing so he said he'd leave him alone for a while. Naruto just sat there the rest for the day in silence until he went to sleep. The next day he was let out of the hospital and noticed there was a note on Ed's scroll which said "Naruto, if I don't make it, I found out who your parents are. Please don't look until you finish everything. Although, you must not read 'resurrection'. Good luck" Naruto gaped and instantly got too work, looking forward to distract himself from Ed and finding out about his parents.
-Timeskip: Two Months-
Naruto had been studying the scroll ever since and finished three days ago. He then spent that time to read the 'resurrection' section just in case it's really easy and he can get Ed back! Once reading it, he found out he could try to do it with alchemy! He decided to read who his parents were first. It said "I only found out about your mother, I'm sorry, you can use this information to ask the Hokage about your mother though. Your mother was: Kushina Uzumaki, the previous container of the Kyuubi." Naruto almost fainted. He finally found out who his mother was!
He spent two days getting over that. After which he spent the next day getting materials that make up the human body and drawing a transmutation circle. As he finished he thought 'I'll just apologise to Ed when he's alive, he'll understand!' Naruto activated the human transmutation circle.
Once it was activated, the circle began to glow a bright golden colour. Naruto began giggling thinking it was working. However soon after, the gold light turned a dark purple, books lying around flew open and windows smashed. Soon enough what appeared to be a gate appeared to be gate appeared to be a gate appeared and when open black tendrils shot out. This was where Naruto realised it had gone way wrong. The tendrils attached too his left leg and it appeared to be sort of dissolved. Before any other limbs could be taken, a red chakra began to leak from Naruto's body, alerting anyone who hadn't seen the bright light that something was happening there.
Soon enough a mob of villagers appeared, with the same three people leading them who killed Ed. Once there, they saw a terrifying sight. The 'demon brat' sitting near a circle without a leg. That wasn't the scary part however, what was the scary bit was the thing in the middle of the circle. It appeared to be a so messed up body it couldn't be called human. And it was still moving until one of the ninja threw a kunai into it and said "The demon is trying to create minions with demon powers! Cut it's arm off and it'll be useless." The Hyuuga of the group quickly walked over to Naruto and noticed he was conscious.
"The demons awake!" another of the ninja quickly ran over saying "Get it's arm, I'll hold it down." He grabbed Naruto and pushed him on the ground so he couldn't move. Soon enough, the Hyuuga began slicing into Naruto's arm, ignoring his wails of agony. Soon after the arm was sliced off and all Naruto had left was a stump the mob left while setting the building on fire in hopes to make the demon suffer more.
The third Hokage and a squad of ANBU soon arrived and began the apartnent with water jutsu. Once the Hokage got in, he couldn't help but gasp. There was Naruto, with no left leg and only a stump of a right arm, with the cut off bit burned black. He was suprised there was no burned left leg but elect that for later, grabbed Naruto and was about to run out when he saw a slightly charred sealing scroll survived. He grabbed it and ran to the hospital.
Naruto soon opened his eyes to see himself in sewer but strangely he still had his arm and leg. He saw a load of pipes and felt he had to follow them so began to walk. Soon he arrived in a large room with a giant cage that had the kanji for seal on it. As he approached he heard "Hurry we have much to discuss." Naruto sped up not knowing what to expect and when he could see through the cage, he saw... a tiny nine tailed fox.
Naruto just gaped and the Kyuubi decided to answer his unasked question "I used a lot of my power to save you then fool, you nearly lost your whole soul. Unfortunately this took a lot of my power so this conversation will be short as I need to rest. Before you ask, this is your mind and yes I am the Kyuubi no Kitsune sealed inside you. Now, when you wake up inform the human in charge of me needing the rest as I won't be able to save you as easily while sleeping, you will only get subconscious amounts of my chakra to heal instead of the usual I send. Now, wake up, I need rest." Before Naruto could say anything he was already fading from the sewer.
When Naruto opened his eyes he noticed he was in the hospital again. However, for once, the Hokage wasn't there when he woke up. Although a note was with a scroll next to it. The note said "We will discuss what happened later Naruto-kun. This scroll was all we could save, I'm so sorry. -Your jiji" Naruto felt slightly better knowing at least his scroll made it out. He quickly unsealed everything and noticed something he hadn't before. It was a small book that said "Ed's map book". he quickly opened it and noticed a note on the front blank page. "Naruto, I'm sure you'll find this eventually, all this book is about is a small map to get to my home from here. Should this ever be important, the place your looking for is "Rockbell Automail Shop" Please don't mess up my book."
Naruto thought 'That's it, I have to get Automail, Ed could live with his... Wait! Ed had his left leg gone too... Do you think he lost it to that gate too and survived somehow? That's why he told me not too... No matter, I just need jiji to let me get Automail.' Naruto decided he'd discuss it with Jiji later.
The next time Naruto opened his eyes, he could see the Hokage sitting there. He quickly yelled "Jiji!" The Hokage jumped startled as he didn't notice Naruto wake up but recovered and said "Naruto-kun... What happened? As you can see, this wasn't a normal attack." Naruto sighed and quickly explained everything that happened. The Hokage was struggling to take it in but said "Okay, now, we can discuss you getting prosthetic arms and legs but I'm afraid you can no longer be a ninja..." Naruto just shook his head and said "Jiji look at this, if you can take me here, I could get this thing called Automail. It's like metal limbs. They really work, it's like Ed's left leg was..." Naruto handed the Hokage the map book and after reading it, he sighed and said "I will have ANBU take you to have a look once you recover a bit. Once you get back from that though you will have too see the council and discuss this." Naruto just nodded vigorously.
A week later Naruto was on a ANBU's back arriving just outside "Rockbell's Automail Shop". They quickly heard a call of "I'll be there in a moment." Soon enough a old woman walked out and said "I'm Winry and how may I help you?" An ANBU was about to speak up but Naruto said "Is this the place that Ed got his Automail? I think his full name was Edward Elric." As soon as Ed was mentioned Winry let out a gasp and said "You know Ed? Where is that idiot?" Naruto sighed and said "Sorry lady... He died a few months ago defending me." The woman let out a choked sob but said "Okay... What can I do for you?" Naruto replied "If possible, I need a Automail right arm and left leg. Also, could you make a artificial chakra network? I know Ed's didn't but he said you could once. "
The woman quickly paled and said "Did you say right arm and left leg? You did human transmutation didn't you? Just like Ed... Okay let's do this." Naruto's eyes widened that he was right about Ed doing human transmutation hits decided to not ask her to live bad memories.
As Winry was setting Naruto up she said "Ed taught you right? I suppose since it was him who taught you it's his fault this happened in a way, I'll give scrap metal to go with this so you can fix it with alchemy so you only come back for resizing or serious damages okay? Now let's get the bandages off." As soon as his arm bandages came off she let out a gasp. "Naruto, I'm afraid this is going to be extremely painful, I have to cut off the remaining bit of your arm okay?" Naruto gulped but nodded. Naruto screamed.
Hours later, when the screaming finally stopped Naruto was sleeping on a bed with his two new limbs. The woman just smiled sadly at him then went outside to inform the people who brought him she was done. Once done with that she began getting the metal ready for them to take with them.
Two days later Naruto had finally gotten used to his limbs and was about to go out to practise alchemy when Winry said "Naruto I believe since you did human alchemy, you gained a special power, interested?" Naruto just gaped at her. The torture of human alchemy gave him something good!? "What is it? Is it cool?" Winry sighed. She then said "Well, after Ed did it, he didn't need circles for alchemy, he just clapped his hands. " Naruto was stunned. If this worked, his alchemy would be fully combat ready...
The next day Naruto was on an ANBU's again as they were about to leave after paying. Winry took the money from the ANBU and gave him a scroll saying "Scrap metal for him to fix his arm and leg. Good luck Naruto. I also thought since you kinda looked like Ed I'd give you a cloak he used to wear when he was a young teen, incase you want to wear it!" Naruto just nodded and waited for her to return, which she soon did with a red cloak. Naruto quickly sealed the cloaked and then the team set off for Konoha. Once they were out of sight Winry began crying as she walked inside saying "Ed..."
Upon arrival in Konoha, Naruto was given a day to rest before called into the council. Upon arrival, he took a seat next to the Homage said he said "Why is this meeting happening?" Soon an elder, Danzo, spoke up "We would like to know the cause of the chakra flux coming from Uzumaki-san's house the other day and need to know if it is a danger to the village." The Hokage sighed and said "I will explain, he gave me details, any questions can be answered at the end."
After the explanation everyone was stunned into silence for a moment until Danzo spoke up saying "I propose Uzumaki-San teaches Alchemy to a elite ninja who can then teach others in order to strengthen Konoha." There were many murmurs until Naruto spoke up "No. I won't teach anyone. What if someone else turned out like Orochimaru with this knowledge? That's a terrifying thought. There's also the fact that people will try human alchemy. It can't be done. People will die without the Kyuubi." There were more murmurs until the Hokage spoke up and said "Naruto-kun I have a question, do you remember any of your attackers?" Naruto thought before saying "Only two and not specifically, only by their clans, the Yamanaka and Hyuuga." As soon as that happened the Yamanaka head looked slightly ashamed and accepting while the Hyuuga jumped up and said "What evidence do you have of it being a Hyuuga boy?" Naruto replied "Well, um, they had white eyes with no pupil and veins bulging around them." Before the Hyuuga head said anything, the Hokage interrupted saying "The Hyuuga and the Yamanaka will be expected to pay half each for the cost of young Naruto's operation for his new arm and leg. Meeting ended."
After the meeting was over Naruto said "Jiji, we need to talk. About my parents." The Hokage sighed and said "I don't know who they are Naruto-kun, I'm sorry." Naruto chuckled and said "Let me inform you of my mother then. Also known as the previous Kyuubi container. " The Hokage paled and sighed "Let me guess, Ed found out and told you?" Naruto nodded and said "Naruto-kun you have to understand my point of view. She had lots of enemies. Not many know, mainly me, the head of the Inazuka clan, the elders and likely the Nara's due to their intelligence." Naruto nodded and said "I understand that the village comes before the villager and I won't tell anyone, however, I will still say our trust is weakened. Can you tell me my father's identity?" The Hokage could only sigh and nod. He then said "When you become a genin I will tell you, it was supposed to be Chuunin but I'll be fair since you know your mothers identity. Now, you should go and rest. Also, before you go, I made the Automail a S-class secret so only the ANBU who took you, me and the council should know. Tell anyone to want, this is if you don't want too. Also, you start the academy in a week." Naruto just nodded and left.
AN: I hope this seems okay, also, as you can see if you read this previously, I have made a few changes due to the fact no matter how mature Naruto is, he still wouldn't be able to understand at all how his father could seal the Kyuubi in him, I plan on him understanding better since he will be older and more mature. I can tell myself Naruto is most likely too mature for his age but I couldn't see someone childish going through having to have the Automail and facing the council. Consider the training he had and Ed's death factors making him mature. Also, I'd like opinions on any pairing? Naruto will likely wear Ed's red cloak unless someone gives me a reason for him not too, if he doesn't wear it, he will keep it as a prized possession to remember him by. Next chapter will likely be a short amount on going through the academy, but mainly graduation and and the Mizuki incident. All reviews are helpful.