A seven year old Uzumaki Naruto was walking around the outskirts of Konoha. The blonde boy, who was wearing a white shirt with an orange spiral on it, along with a pair of dark blue shorts, as well as three strange whisker-like marks on his cheeks, had just pulled his greatest prank to date, releasing a bunch of harmless garter snakes into the girl's bathrooms at school. Of course Iruka-sensei had caught him and he was punished, but he didn't care. At least he was getting some acknowledgement, although he didn't like the idea of being known solely for his pranks.
Out of the corner of his eye, Naruto saw a dark clad figure lying on the ground in the warm weather and light breeze that made the leaves of the trees rustle in a kind of exasperated way. His mouth twisted into a grin at the fun he could have with the sleeping figure. Naruto crept silently towards the slumbering figure; pen in hand, ready to draw all over the unsuspecting victim. However, when he reached the side of the soon to be victim of his prank, he noticed that the man was staring at him with a blank look in his eyes.
Naruto froze when he saw this and started to mumble an apology to the man.
"Ah, sorry, I was just…yeah, um sorry? No hard feelings right?" The boy asked the man, not making eye contact.
When he heard no response, he looked at the man, expecting to see the cold furry that people always have on their faces after his jokes. Instead, the man was lying on the ground in exactly the same position he had been, when Naruto first saw him.
'What is he, sleeping with his eyes open?' Naruto thought, a sweat drop forming on the back of his head.
Still searching for a prank to pull, Naruto settled for the 'kick someone in the ribs and run away' gag. An oldie but a goody. Naruto drew his leg back and delivered the hardest kick, a seven year old could manage. He expected the man to get up and chase him, but instead he simply lay there. Once again walking over to the prone figure, Naruto looked at the man's face, only to notice that it was turning slightly blue. In a moment of clarity, Naruto realized that the figure wasn't sleeping. He was dead.
Shocked at his new found discovery, Naruto turned around to run away, only to find his path blocked by another figure, this one in an ANBU uniform. Naruto was frightened right then, he normally got blamed for things he didn't do, and this was something he didn't do. Hell, he didn't even know what happened, other than he found the guy dead.
"I-it isn't what it looks like." He exclaimed quickly, "I just found him…"
"I know exactly what it looks like." The ANBU said, walking over to the body. Naruto could see that the shinobi had dark black hair, much like the dead man had. "Uchiha Shisui appears to have been suffocated or drowned. Killed by Uchiha Itachi." The masked ninja replied.
"That's awesome, how you can tell that just by looking at a dead body!" Naruto exclaimed, glad that he wasn't being blamed for the death of the man. "How do you do that?"
There was a pause for a moment, as the ANBU turned and looked at Naruto, his eyes turning from black to red, with three odd marks circling his pupils.
"Because I am Itachi." He stated calmly. "Now that you have seen this, I cannot let you live." He said as he drew his sword.
Naruto turned to run, but was stopped when the cold metal of an ANBU sword cut through his stomach. The sword was quickly removed, before it was once again slid through his body. Naruto let out a scream, only to find it muffled by the hand of the ANBU. As Naruto slid to the ground he was rolled over. Before he lost consciousness, he saw the ninja take out a kunai. Then everything went black.
The next thing that Naruto knew, he was lying in a bed in a hospital. However, having never been hospitalized before, he didn't know where he was. He tried to open his eyes, but found that he was stopped by something covering them. Reaching up to touch his eyes, he felt the course but soft texture of gauze. Suddenly he was racked with a fit of pain as the adrenaline of his awakening wore off. He groaned and winced in pain, it wasn't until someone spoke up that he realized someone was in the room.
"Naruto-kun, it is good to see you are awake." Said Sarutobi, the Sandaime Hokage.
"Uhh, oji-san, what happened?" Naruto managed to groan out while he winced.
"It would seem that you were attacked by Uchiha Itachi and thrown in the river, left for dead." Sandaime said. "You were found floating in the river along with the body of Uchiha Shisui, by an old student of mine, and she brought you both back."
"Hey, old man, what's with my eyes?" Naruto interrupted the venerable Hokage.
Although he couldn't see it, the Hokage cringed before he answered.
"I was about to explain that. It seems that for whatever reason, Itachi damaged your eyes beyond our healing abilities."
This elicited a gasp of shock from Naruto.
"Does this mean I'm blind?" He asked, through gasps of breath. He began to cry at the prospect of never being able to see again.
"Actually, far from it." The old man said. "My former student is a very good medic-nin and she was able to transplant Shisui's eyes into you. It is very rare indeed, but it was vital to your survival that every place that blood could leak out from was plugged. That included your eyes."
"Eww, I have some dead guy's eyes in my head!" Naruto yelled.
"Yes Naruto-kun I suppose you do." The old man chuckled. "Naruto, those eyes are very special, they hold the bloodline limit of the Uchiha clan."
"What's a bloodline limit?" Asked Naruto.
"It's a special ability that is passed down through someone's family." Explained they gray man. "Now, since you are not an Uchiha, I do not think that the limit will awaken in your eyes, but that doesn't mean that they aren't valuable. If someone were to take them, Konoha would be in very big trouble."
Naruto just lay in bed digesting all of the new information he had just learned.
"Old man, how long was I out for? Did anything important happen?" He asked.
"To answer your first question, you were unconscious for about two weeks. Now, Naruto, the second thing is pretty bad. Itachi, the man that attacked you, he murdered his entire family except for his little brother, Sasuke." Sarutobi said in a sad voice. "This means that there are only four people left in the world with the same kinds of eyes you have."
Naruto just sat there in silence. He didn't know what to do, he was only seven for crying out loud, and he just found out that he had some dead guy's eyes in his head, and the dead guy's family was dead, except for one kid. This day just couldn't get any weirder. Oh how wrong he was.
After checking up on Naruto, Sarutobi made his way back to his office, he had a meeting to conduct with someone, and it wasn't going to be good. As he entered his office, he saw his old student, Tsunade waiting for him. She was holding a standard medical file, with all of the information they could gain from Naruto while he was unconscious.
"Everything seems to be fine, Sarutobi-sensei." The blonde women said. "There is one interesting thing. You said he was an orphan, right?"
The Sandaime just nodded.
"Well, I ran a DNA test with some extra blood samples we had, and well…you should look at them yourself." She handed the old man the folder. When he opened it he stared at a complete genetic profile of the blonde. However, what grabbed his attention was the report that Tsunade had written up.
"Who else has seen this?" He demanded.
"Only Shizune and I have seen the report." She stated, calmly.
Sarutobi began to massage his temples as he felt a migraine coming on.
"Do you know how this could have happened?" She asked.
"I have an idea, although I shudder to think of how she'll take this." Sarutobi said.
He pressed a button on his intercom and waited for his secretary to respond.
"I need you to have Mitarashi Anko meet me as soon as possible." He ordered.
The aforementioned jounin was currently training out at field thirty-eight. Mitarashi Anko was a kunoichi known for her short temper, more than slightly sadistic nature, lack of proper clothing and her prowess with kunai knives. She was a little annoyed that the hokage was pulling her away from her training, but she needed a short break anyways. He brown trench coat didn't move at all as she made her way up the winding stairs. When she entered his office, she was greeted by the sight of the old man, as well as Tsunade, the legendary medic sannin.
"You wanted to see me Hokage-sama?" She asked, a look of slight confusion passing through her brown eyes.
"Yes, as you know, Uchiha Itachi attacked and killed his best friend as well as a small boy a couple weeks ago. Tsunade ran a blood test, to look for any possible relatives."
Anko didn't like where this was going. There were only two reasons why he would call her in to discuss this kind of situation.
"Anko," The sandaime said, breaking her train of thought. "We have good reason to believe that it's him."
Anko's eyes grew wide at those words, and she collapsed into a chair, grasping her breath and shaking her purple-tinted hair in such a manner, as if to knock loose a certain memory.
Tsunade thought this was strange, even for Anko, who was known for her loud entrances and more than slightly sadistic nature.
"What do you mean him?" she questioned. "What in the hell is going on?"
Sarutobi sighed at the question of his student.
"During the Kyuubi attack, there were many S-class secrets made, one of which was Anko's pregnancy." He stated.
"What do you mean, pregnant, she's only twenty four, that would make her seventeen, at the time, I know that's rather young, but that's not exactly worthy of such secrecy." Tsunade said, angry that she was left out of the loop.
"You know who Anko's jounin sensei was, don't you?" Sarutobi asked, rubbing his head. "You know what he did?"
Of course Tsunade knew this, Anko's jounin sensei was Orochimaru, her former teammate turned missing Nin. He was wanted for experimenting on humans, but she didn't see what that had to do with…
"Oh, my god." Tsunade gasped, looking at the slouched figure resting in a chair, her hands grabbing her stomach.
"Yes, due to one of Orochimaru's experiments, Anko hasn't aged in over seven years." Sarutobi said, trying to comfort the sobbing women in his office. "And due to another of his experiments, she found she was pregnant." We think it was part of an experiment to create a new bloodline limit."
"So, you're saying, that my baby is alive?" Anko asked, through ragged breaths. "Why? Why did you lie to me than?" She demanded.
"Anko, I had no intention of lying to you about this, when I found your son, there was no evidence that he was related to you in any way, and due to the damage of the Kyuubi, we just assumed, that your son was dead. I'm very sorry about this."
"I want to see him, right now!" Anko demanded. "There's no way, that I'm leaving him now, who knows what he's going through because of me?"
"Of course Anko, but before that, I have a few other things I want to discuss with you first." The hokage instructed.
"All right, but can you at least tell me his name." She said.
"His name is Uzumaki Naruto." The third replied, watching her reaction.
Anko's face was a mixture of emotions. Happy and sad were interchanged with anger and fury. She was grateful for the chance to be a part of her son's life, sad that he had been hospitalized in critical condition for the past two weeks, and angry at the villagers, who were too ignorant to see that the boy, her son, wasn't the demon that was sealed into him.
"Anko, in the DNA results, Tsunade found some very interesting information. It seems that Naruto has a large number of genetic markers, in common with the Yondaime."
This elicited a loud gasp from Tsunade and a blank look from Anko.
"Are you saying that the father of my son is…is the Yondaime?" She questioned.
"No, I'm not. You see, during his assault, Itachi damaged his eyes so badly, that they had to be removed. When Tsunade found him, she had to transplant the eyes of Uchiha Shisui to stem the large amount of blood loss he was experiencing."
"I don't see why that is important; Kakashi has a sharingan implanted in his head too." Anko growled.
"Yes, but Kakashi hasn't suddenly developed Uchiha genes." The third replied.
"What do you mean Uchiha genes?" Anko questioned.
"Hear me out, when your son was born, he had darker hair right?" The third questioned.
"Yes, dark hair and my eyes." Anko said.
"After the Kyuubi was sealed, the boy I found had blonde hair and blue eyes. Just like the Yondaime. In fact, he looks exactly like the Yondaime did at his age. Now, with the Uchiha genes, his hair is still blonde but with black streak in it, and his eyes are going to be black. His DNA shares markers identical to Shisui, as well as the Yondaime. What I think happened, was that Orochimaru succeeded in creating a bloodline, that would absorb anything foreign that the body was subjected to, into the DNA. That way, any descendants of the child would bear the traits as well." Sandaime concluded. "I think that before my successor died, he may have transferred, either by accident or intentionally, some of his DNA into Naruto, giving him his former appearance."
"Wait, what about the Kyuubi, does that mean that he is part demon or something?" Tsunade asked, shocked at her sensei's analytical analysis of Naruto's abilities.
"My son isn't a demon!" Anko said, loudly, glaring at the sannin.
"Calm down you two." The sandaime said. "If I am correct, Naruto must be subjected to someone's DNA to change. Since the Kyuubi is sealed inside of him, than there is no fear of him becoming a demon, besides, we have a full DNA write up. He's 100 per-cent human."
"But, what's to stop someone, from putting their blood into him. He'll keep on changing, and that won't be good." Anko worried that her son may end up with some kind of disorder before she got to know him.
"Well, for one, since the Kyuubi is healing him, it is safe to assume, that the demon has some ability to regulate what is absorbed and what isn't. If he didn't have the Kyuubi, than I shudder to think what would happen." Sarutobi said. "I believe that the ability is either fading, or slowing down completely, because he adopted the genes of the fourth within a matter of minutes, but this time it took almost the entire two weeks he was unconscious for the changes to occur. Do you have those reports, Tsunade?"
"Hai, his DNA had been slowly changing over the period of the past two weeks, and the changes were mostly minimal. I would need to run more tests, but I think that this ability is either being over written in his own DNA, or it is being stopped as to prevent further damage to the boy." The medic Nin deduced.
"Now," said the third Hokage, "What do you say, about meeting your son?"
(A/N: I figured I'd outline Naruto's bloodline limit.
Senshin (absorption) - Naruto's bloodline limit allows him to absorb any foreign DNA introduced into his body. This allows him to pass on the traits to his children, as well as use any features like the mangekyou sharingan. (That's not a hint. It's just an example) He has genes of Anko, the Yondaime, and now Shisui. No one knows who his father is.
This is going to be a longer story than my other one, hopefully since I'm giving myself a longer time line, and I have no clue as to any future pairings. Feel free to suggest any thing, since I only have a mediocre idea as to the final shape of the story. Thank you, and please review. I can't get better without them.)