Seen so damn many of these that it should have dissuaded me from making a new one, but whatever. This story, if the title was not indicative, is about the Rinnegan, and everything leading up to it.

Danzo Shimura looked through the window into the observation room as his ROOT medics finished up the process of implanting Fugaku Uchiha's Sharingan eyes into the unconscious jinchuriki. He would make the perfect asset. With his already Jonin-level reserves the boy would be able to use his Sharingan almost indefinitely. Combining that with the Senju DNA already making up the boy's body due to his Uzumaki heritage and this child had the potential to become an S-Class shinobi. And the best part was...

Danzo wouldn't have to do a thing.

He would allow the boy to continue his life as a moron until he fell into a situation in which he would use the Kyuubi's chakra in defense or offence, Danzo didn't care which. The potency of the demonic chakra would burn off the variation of the caged bird seal that Danzo would be applying himself. The seal was designed to keep his Sharingan sealed and change their color back to the blue the boy was known to have. By the time Naruto went on a mission of significant difficulty that would force him to use the Kyuubi's chakra he would have enough chakra of his own to maintain the Sharingan without any drawbacks.

One might ask what Danzo was planning on doing once news spread of Naruto's Sharingan and how he obtained it. Well, as it turned out, he would do nothing.

Even if the transplant was traced back to him by Sarutobi, Danzo would probably be dead by then anyway. As it turns out, the disease which Itachi had contracted on a mission out of the village was a viral necrotic lung infection that was contagious and had no known cure. Simply put, Danzo's lungs were dying, and him along with them. He didn't know why his case was spreading faster than Itachi's was, but it didn't even matter. The Uchiha clan would be on the brink of extinction due to this virus even if Itachi hadn't slaughtered them.

Danzo's imminent death had put things in a new perspective for the old war hawk. Right now he was focused on two things; making the jinchuriki as strong as possible, and getting his ROOT soldiers back into the habit of showing emotion. They would need it if they were going to be reintegrated back into the village shinobi force properly. They also needed to be able to think on their own, if they were going to put their skills to use without him pulling the strings.

He looked back to the child on the operating table as they finished healing the Sharingan into Naruto's skull. He would be Danzo's last service to his village. He wanted to create the perfect weapon, but he would have to settle for a jinchuriki with the power of the Sharingan. Who knows, he might even unlock the Mangekyou Sharingan. A shinobi's life was full of despair after all, and the death of a comrade would hit a naive and isolated boy like Naruto harder than most.

XxxxX

Naruto awoke in his apartment with his eyes on fire. Not really, but it sure felt like it. He couldn't keep them open for longer than a second, the pain was just too intense. Walking to the bathroom he looked in the mirror and held his right eyelid open with his fingers so he could get a better look.

The sclera was red and irritated and his normally vibrant blue irises seemed to be a shade darker than usual. That could just be his imagination though. He sighed and looked at the clock on his bathroom counter only to realize that it was 9:14. He was late. Great.

He quickly got dressed and put his goggles on his head before walking swiftly to the door. Just as his hand reached for the knob he found it turning. Taking a couple steps back he pensively waited for the door to open. Hopefully it was just the Hokage and not another group of villagers waiting to beat him up.

Turns out it was neither. An ANBU walked through the door and jumped slightly when he saw Naruto standing in the middle of the room, "Uzumaki-san, where have you been? Hokage-sama has been looking for you."

Naruto was perplexed, "What do you mean? I was here all morning. Is it because I was late for the Academy?"

Tora frowned behind his mask, "Come with me, we need to see the Hokage." he said before putting his hand on Naruto's shoulder and they disappeared in a puff of smoke.

XxxxX

Hiruzen Sarutobi felt the chakra of one of his ANBU before there was a puff of smoke which cleared to reveal Tora with his hand on Naruto's shoulder. The Sandaime narrowed his eyes, "Where have you been Naruto? The village is in nigh panic over first your disappearance and then the incident with the Uchiha clan. Many are starting to say that you had a hand in it, despite my assurances otherwise."

"Ok, what incident? And i didn't disappear! I came home from the academy yesterday, went to bed, woke up with my eyes hurting like hell, was about to go to the academy because i was late but then your ANBU dude took me here." said Naruto defensively.

Hiruzen pondered over Naruto's story, even if he believed it, it just didn't add up, "Naruto, you have been missing for over a week, and the day after you disappeared the entire Uchiha clan was massacred by Itachi Uchiha. People who dislike you are generally pointing fingers at you."

Naruto's eyes were wide, "Wait Sasuke's clan was murdered? By his brother? This has to be a joke! Sasuke always talks about how cool and nice his big brother is. There's no way he would do something like that!"

"Well regardless it happened, and I'm suprised you haven't heard already. Which brings up the point of where you were. And why you don't remember anything." said Hiruzen inquisitively, "You said your eyes were hurting this morning, maybe they will have a clue as to what happened. Were going to the hospital." Hiruzen walked around his desk and put is hand on Naruto's shoulder before once again disappearing in a puff of smoke.

XxxxX

They appeared in a stone room with torches on the walls and strange symbols on the floor. Naruto was confused, "I thought we were going to the hospital, why are we here?"

Hiruzen looked at Naruto, "This is the hospital, or more specifically, it's the sealed off room beneath the hospital that only the Hokage, ANBU and head medic are allowed into. It's for sensitive and classified medical matters. You sit in the middle of that seal and I will get the head doctor."

The Sandaime left through the large metal door at the front of the room and Naruto sat down in the middle of the circle on the floor that was surrounded by what Naruto now recognized as Fuinjutsu, an obscure ninja art that Naruto knew was used for sealing things in scrolls and making exploding tags, but he didn't know what the seal on the floor was for.

The Hokage and another man walked into the room and Naruto immediately asked, "Oi, What's this seal for? I'm not sitting on a storage seal am I?"

The other man laughed, "No, that's a Medical resonance seal, it shows me everything in your body from veins and arteries to seal tattoos, but i imagine you don't have many of those."

Hiruzen nodded, "He said his eyes were hurting this morning, and he can't seem to remember the last week and two days."

The medic nodded before he made several hand seals becore putting his hands on the edge of the seal, which began glowing with green light. He frowned as he saw two things which unnnerved him, "What is the meaning of this Hokage-sama? He has eyes that aren't his, and what sort of looks like a caged bird seal on his forehead giving off a layer of chakra changing the appearance of his eyes."

The Hokage looked sharply at Naruto before calling off the seal, walking up to naruto and putting his hand on his forehead, injecting chakra to disrupt the flow of the seal. He and the medic gasped, and Hiruzen shouted, "Naruto! Tell me where you have been for the last week! How do you have the Sharingan?!"

"The what? What's a Sharingan? I don't remember what happened, i already told you everything." said Naruto nervously as he had never seen the old man this angry at him before. He noticed his eyesight seemed sharper for a moment before going back to normal, the seal back in place.

Hiruzen deepened his frown, "I think i know what's going on, my old teammate has a hand in this, i can feel it."

I have been wanting to make one of these for a while, tell me what you think in a review.