Since, I've been having writer's block on my Pokemon story's, I've decided to write this. This definetly going to be the darkest story I've ever written, anywhere. This story originally was HaremNoJutsu's "Rinnegan: Eyes of God," which I've obviously taken over since they haven't updated it for years. However this also contains elements inspired by dracohalo117's Kushina's Love, Naruto's hate. It should be noted that in this story, Nagato/Pain and Kushina are brother and sister, and the Uchiha massacre is committed on Naruto's fifth birthday. Only about 5% of this is my original writing. For the other 95%, I credit dracohalo117 and HaremNoJutsu. Enjoy.

Naruto was sitting in his room…well; it was more like a cellar closet. The floors were hard, cold, and uncomfortable, and the only thing he had to keep himself warm was the clothes on his back, which were too small for him, and moth eaten.

He looked at the ceiling and cried, "H-happy b-birthday…t-to m-me…h-happy b-birthday…t-to…me…" he curled his feet into himself as he sobbed.

"SLAM!" the door to his closet was thrown open and he was dragged out by his hair. He was thrown onto the ground as the air was knocked out of him.

Standing above him, Kushina was stumbling over herself, the tell tale smell of sake rolling off of her, "Y-you…demon!" she kicked Naruto in the stomach as she grabbed a stake from the wall, "How dare you sing when you KILLED My Husband!" she grabbed Naruto's hair and sneered, "You filthy beast!"

She stabbed the stake into Naruto's chest, making the young blond scream in agony.

Kushina slapped him as she finished carving Naruto's chest up, "I am ashamed to have birthed you!" she stepped on his hand and began to apply even more pressure, "The only reason you live here is so you can work off your redemption for killing my husband and child!" Kushina spat in Naruto's face as she brought her foot back to kick him again, "Be glad I have a kind enough heart to let you live under my roof!"

Just as Kushina was about to kick Naruto, he closed his eyes as he felt a burning sensation. When they opened, the blue that was there disappeared. Instead, the eye now had a gray scelera, a black pupil, and a series of rings making a ripple-like pattern. Instinctively he yelled out "Shinra Tenshi!"

The effect was instantaneous. Kushina was flung backwards to the wall, dazing her. Naruto sprang to his feet and raced up the stairs. Turning back to her, he yelled out "You don't want me here! Well good! I'm leaving this hellhole and never coming back!" He slammed open the door and ran out of the house.

The last thing Kushina saw before she passed out of shock was Naruto's eyes, which looked betrayed, sad, and angry... all directed at her.

"Sasuke... Don't come in".

"What?" Sasuke screamed as he burst through the door, "FATHER! MOTHER!" he shouted as he noticed their bodies on the floor.

"I warned you Sasuke" Itachi spoke as he stepped out from the shadows.

"BROTHER! Father and Mother are dea- ..." Sasuke stopped halfway as his mind registered what had happened.

"YOU KILLED THEM! Why?" Sasuke roared as he charged towards his brother, only for Itachi to seemingly faze out of existence and appear before Sasuke, his fist planted in the young boy's stomach.

"You want to know why? Fine, I'll tell you, this clan disgusts me, killing each other over such trivial things, power, authority, it's pathetic. If anything, the last 3 Ninja Wars have shown us that nothing good ever comes from obtaining such things at such a high price, namely thousands of people dead, but this doesn't seem to matter to a clan as fickle as ours, they were planning a coup to take over Konoha, and destroy everything so many people died for." Itachi angrily proclaimed.

Sasuke collapsed on the ground, being violently sick, before running to the door. "DON'T KILL ME PLEASE" he screamed.

Itachi calmly walked up to the boy, grabbing hold of his shirt and turning him around to face him. Before, surprisingly, smiling at him and telling him; "I'm not going to kill you Sasuke, you knew nothing of this, I had hoped I'd be able to make it away without confronting you, I'm leaving the village, to join a group that wants to bring peace to the world, I refuse to stay here. There are only a select few people who I respect in this village, who they are is information I'm not ready to divulge to you yet. Become strong little brother, and when you feel ready, leave the village, I will find you and we shall talk again. Goodbye. I'm sorry."

With that, Itachi struck Sasuke once more in the stomach, causing the boy to topple over unconscious. Itachi was already gone before his body had reached the floor.

Streets of Konoha:

Itachi was currently sprinting along the rooftops of Konoha, 'It should only take another 2 minutes for me to reach the gate, then I can –', He was shook from his thoughts when an enormous chakra spike radiated around the area. 'What on earth was that?' He decided to trace the chakra back to where it had first come from. He looked down from his vantage point.

"Haha, take that demon!" One of the villagers screamed as they kicked him square in the chest, easily winding him. Naruto had stayed silent throughout the entire ordeal, deciding not to give them any satisfaction. He noticed they parted as a man came forward with an iron pipe in his hands, his eyes widened as he realized the man was going to use it on him. The man stepped forward with a smile on his face, and was about to bring the pipe down onto Naruto's legs when he felt something throw him back, his eyes widened as he coughed up blood, feeling his ribs shatter inside his chest, as he was flung back and into a wall, he looked up briefly to notice the entire group he was with had also been launched backwards, there were corpses everywhere, their arms and legs snapped in grotesque ways. He died a moment later.

Itachi, who had been watching the ordeal, was about to intervene when he saw the man raise the pipe above his head, when he suddenly felt himself being pushed backwards by an unknown force, he had recovered quickly and gone to down to street level to survey the carnage, he was shocked by what he saw;

A small crater laid in the centre of the street with Naruto lying in it, looking around dumbstruck by what had just happened. Itachi walked over to the boy. "Naruto-kun are you alri-?" Itachi was about to ask him if he was alright when he caught sight of the boy's eyes.

'What is this? This is impossible!' He thought 'That ripple like pattern, I've read stories about it from scrolls in the Library, I thought it was a myth? They were supposedly possessed by the Rikudou Sennin, God of Shinobi! The Rinnegan! This boy, who exactly is he?' Itachi was shocked by this new discovery.

Naruto looked around, his vision was strange, he could see chakra, or at least that's what he thought it was, if he focused enough he could see behind him, he noticed there was someone standing in front of him and he held his hands up to defend himself. "Please don't hit me again!" He had finally cracked, seeing what he'd just done.

Itachi smiled at the boy. "Naruto-kun, I'm not going to hurt you, I have a feeling the people who you killed families might though" Itachi thought about what he was going to ask the boy next and wondered if it was ok. 'He's got the eyes of God, I'm sure they'll let him join, he's not welcome here in this village anyway, ignorant fools'. "I'm leaving the village, would you like to join me Naruto-kun?" Itachi asked.

To say the least, Naruto was shocked by what this man was asking him, he was also curious as to how he knew his name but that would come later, he thought about what the man offered. 'Leaving the village? I'm not exactly welcome here but still, what about Kakashi, Jii-san and Ero-Sennin, I don't want to leave them.' Naruto thought.

"Will I be able to come back and visit?" Naruto innocently asked. Itachi smiled at the boy "I'm sure in a few years time, you'll be back" He answered.

"Alright, should I get anything from my apartment before we leave?" Naruto asked.

"Any food you wish to take, we'll be eating on the move so nothing heavy. You will speak to no-one, if you do encounter anyone, ignore them and keep running. I'll give you 10 minutes; meet me at the North Gate." Itachi told him.

Naruto simply nodded before sprinting back to his apartment; luckily for him he didn't encounter a soul. He quickly packed various snacks and a change of clothes before leaving the key on the table and closing the door behind him.

At the North Gate:

Itachi was standing there, waiting for Naruto, he knew the boy would come, and his hopes were confirmed when Naruto came running around the corner. He skidded to a halt in front of him.

"Alright, let's go going." Naruto said.

Itachi merely nodded. "I'm sure you're curious why I'm leaving the village. I'll explain them to you soon as I know we're safe, for now follow me" He said before launching into the trees, Naruto following closely behind, easily keeping up with him.

'Just what else can those eyes do?' Itachi thought to himself as he remembered the directions of the map he'd been given, telling him how to reach Amegakure from Konoha.

4 hours later:

"Naruto, let's stop for a little bit, I think we're far enough away from Konoha to stop without needing a constant look out, I'd also like to ask you some questions, if that's ok?" Itachi asked.

Naruto stopped, catching his breath, before helping Itachi find a clearing where they could rest for the night.

"What supplies did you bring?" Itachi asked him. Naruto opened his pack and showed Itachi what he'd brought. There was some slightly crushed Onigiri and a few bottles of water.

Itachi looked at him for a moment. "Hmm, it's to be expected that you didn't know what to bring. Go and gather some firewood and I'll prepare what food we have. I'm afraid we can't stay still for long, but I'd like to you to answer those questions now." He told him. Naruto nodded and headed off into the forest.

Within five minutes, Naruto had returned with some reasonably sized branches that looked like he'd snapped them in half, and plenty of smaller twigs. Itachi was quite impressed by this. "Naruto, how did you know exactly what kind of things to collect?" He inquired.

"Oh, I went to the library and read a lot about Ninjas, I was going to enrol in the academy the day I turned 10, so I could prove to the villagers that I want to help them, not destroy them as they always seem to think" He replied sadly.

"I understand" Itachi replied, nodding his head slightly.

"Now Naruto, do you feel any different since what happened in the street?" Itachi questioned.

Naruto took a few moments before answering, "Yeah, I feel great, but my eyesight has become all strange and distorted, I think I can see chakra. It looks odd, around your body I can see these strange blue swirls, do you have any idea of what they are?" Naruto finished with a question.

"It's chakra Naruto; you don't see anything else, just the swirls?" Itachi asked.

Naruto just nodded. "I can only see the blue swirls; they're inside your body as well. Am I supposed to see something else?"

Itachi just shook his head. 'That's surprising, they can only see chakra.' He thought.

"I want you to take a look at this." Itachi said as he handed Naruto his forehead protector. "Look at your reflection."

Naruto did as he was told and almost collapsed. "What's happened to my eyes?" He roared.

Itachi smirked before speaking, "It's called the Rinnegan Naruto, it's a legendary Doujutsu, said to be possessed by the man who discovered the true use of chakra and invented Ninjutsu, The Rikudou Sennin. I don't know anything about it apart from the thing we've just learnt, that you can see chakra. I'd also like to check something out when you've calmed down a bit more."

Naruto was currently staring at his reflection on the forehead protector; he gradually began to accept the way he looked, before moving the forehead protector closer to his eyes. 'Hey, they look pretty cool' He thought to himself.

"Right, let me get this straight, I have a legendary Doujutsu, called the Rinnegan?" Itachi merely nodded, "It was said to be possessed by the man who invented Ninjutsu?" Itachi nodded once again, "Well, I've got to say, THAT'S AWESOME" Naruto shouted as he started laughing, Itachi had a slight unnoticeable smile on his face.

"It's quite ironic really, a boy who was constantly beaten and ostracized for something that was out of his control, will likely become one of the strongest ninja of all time." Itachi stated matter-of-factly.

Naruto stopped laughing after he heard what Itachi had just said, and just sat there for a few moments with his mouth agape, this caused Itachi to smirk and added, "Even if I reach my full potential, if you Naruto are to reach yours, I will not be able to defeat you, I doubt anyone in the world will be able to stand against you, however, don't think this will just fall in your lap, you will have to train for many years to achieve that level."

Naruto merely nodded before remembering what Itachi had said earlier, "What is it you wanted to check out, Itachi?" he asked.

"Oh yes, I just wanted to see if your new eyes could detect Barrier jutsu as that will be extremely effective if you are sent on Reconnaissance missions. Step back a few feet and let me use one, tell me if you noticed anything different." Itachi said.

Naruto nodded and stepped back.

"Kekkai: Tengai Hōjin" Itachi shouted after performing a few hand seals.

Naruto noticed it immediately, "I can see it, it's some sort of dome surrounding you."

Itachi was surprised, "I see, so you can see Barriers as well? That's interesting."

Naruto just smiled before sitting down again.

"Oh yea, Itachi, why were you leaving the village?" Naruto asked.

Naruto noticed Itachi flinch at the question before he settled down on a log, and gave his answer.

"I wiped out the Uchiha clan" He replied simply.

Naruto was shocked at this, not expecting such a blunt answer.

"They were planning a coup, and were attempting to take over Konoha, if they went ahead and did that, other countries would most likely get involved and attack Konoha without warning or repercussion. You haven't seen war, you don't know what it's like to see hundreds of people dead around you, it's terrifying. I did what I had to, to prevent a disaster." Itachi told them.

"I did however, leave my younger brother Sasuke alive, he will join the organization we're going to when he feels he is ready, he knows of the coup, it'll be up to him whether or not he accepts it, if he doesn't and decides to hunt me down, I'll kill him." He added before beginning to pack up his supplies and putting out the fire.

"Come, we have at least another day of travelling ahead of us, we've wasted enough time as it is." Itachi said as he slung his backpack over his shoulders. He quickly stamped out the fire, spreading dirt over where it had been.

'They're sure to notice this, but we have, at least, an 8 hour lead.' Itachi thought.

Naruto nodded before standing up and dusting himself down. Within moments Itachi had launched into the trees, with Naruto fresh on his trail.

The Next Morning, in Konoha:

"Hokage-sama! Something terrible has happened" A Chuunin rushed into his office.

"Yes, I already know about the Uchiha massacre, I also know that he's taken Uzumaki Naruto with him, leave me" Hiruzen replied without even turning toward the person who'd entered his office.

"Huh, so it's true then" A voice from outside the window called out.

"Yes, apparently the villagers decided to attack Naruto yesterday evening, Naruto killed them and joined Itachi. Hiruzen answered the voice.

Jiraiya then jumped up and landed on the windowsill, "He killed them you say? Was it the Kyuubi?" He asked Hiruzen.

Hiruzen shook his head, "No, they were killed by some kind of technique I've never seen before, it seemed like their organs were pushed back, the force must have been immense since all of their ribcages are shattered and there are several bodies with severally broken bones."

Jiraiya's ears perked up at this. "I see, would you mind if I had a look at the bodies? That description reminded me of something I've seen once before." Jiraiya asked.

Hiruzen merely nodded his head, before handing Jiraiya an access pass to the Hospital Morgue.

"I'll speak to you about it later." Jiraiya said before jumping out of the window and making his way towards the Hospital.

Morgue:

"This – this is exactly the same as before! The bruising on the chest, the organs scattered around the chest cavity like someone's taken them all out and put them back in however they please. Well, Uzumaki Naruto, you certainly are an interesting child, I look forward to our next meeting." Jiraiya said to himself as he walked out of the Hospital, heading towards the Hokage tower to report his findings.

Hospital:

Meanwhile in a private room, Uchiha Sasuke was lying in his bed thinking about his brother had said; 'They were planning a coup? Why would they do something like that? We were the strongest clan in Konoha! Now that I think about it, Father had been acting rather distant lately, and Itachi was acting strange as well...Itachi, he theoretically saved my life, I need to think about this more'. He sighed before lying down and dozing off.

Near Amegakure:

"Ok, we're nearly there" Itachi spoke; he could barely be heard over the sound of the pouring rain.

"The sooner we get there, the better" Naruto grumbled.

Amegakure:

"Eh?" A voice shouted out.

"What is it?" A gentle female voice asked.

"Itachi has arrived, but it seems he's brought someone else along with him, their chakra is almost double mine!" The voice replied.

"What? How is that possible?" The female voice asked worriedly.

"I don't know, Konan, go and meet Itachi, it seems they all entered the village at the same time, so once you find him, I'm sure you'll encounter the other two." The voice told her.

"Hai, Nagato". Konan replied.

"Be careful" He warned as she was making her way out.

She merely nodded.

Entrance to Amegakure:

"Halt! What is your business here?" The Gate guard questioned.

"My name is Uchiha Itachi, this boy here is my travelling companion, we seek entry into your village, our reasons are our own." Itachi replied.

"You will state your reasons for being here, or you will be treated as an intru-" The Gate guard had already raised a Kunai to defend himself.

"Stand down, Masuyo, leave them to me" A woman had appeared behind him.

"A – Ah, Konan-sama, I will do as you say! Forgive me!" He bowed his head quickly before returning back to his post.

"My name is Konan, I am an emissary for the leader of this village, state your business." Konan told them firmly.

"My name is Uchiha Itachi, your leader is expecting me, these two people here are my travelling companions, and I request they be allowed in as well." Itachi told her.

Konan knew of Itachi's arrival, she just had to confirm it was him. She then took a glance at the other boy; he had his head turned around as he was looking around the village. She could feel power radiating off him; she cleared her throat to gain his attention. He turned towards her and she froze on the spot.

'What! This cannot be, he's got the same eyes as Nagato! I see, this is the chakra he was talking about, he'll be a worthy addition to Akatsuki, perhaps even stronger than Nagato.' She thought to herself.

He grinned at her and said "Hey, my name's Uzumaki Naruto, nice to meet you!"

She suddenly felt a faint smile tug at her lips, before she pushed it to the back of her mind and dropped back into her serious demeanour.

"Hai, now come with me, I'm sure our leader will want to meet and greet you both personally." She stated.

She nodded to Masuyo, and he responded, allowing the three of them passage and recording their names within the journal on the desk in front of him.

They walked through the gates into the city of Amegakure itself. All three of them were taken aback by how the city looked, although only two of them showed a surprised looked upon their faces. Itachi remained stoic as ever.

"Whoa, this place is amazing" Naruto spoke, voice filled with awe as he glanced upwards, his sight filled with towering skyscrapers.

It was at this time; Naruto had cast his gaze upon Konan, and noticed what she was wearing.

"Hey, Konan-san, I like your cloak" He said. She just carried on walking; neither of them could see the faint smile on her face.

They continued on through the city, with Naruto making stupid remarks almost constantly throughout the short journey.

They soon reached the entrance to the highest tower in the city and Konan stopped abruptly in front of it.

She turned and spoke to the two of them: "We're here, through this door lies your future, are you willing to proceed?"

She was surprised by how quickly Naruto responded. Satisfied, she gathered some chakra into her hand, and placed it across the barrier in front of the door. Once the barrier had finished dispersing, the doors opened themselves and they stepped inside.

They walked into a strange foyer, noticing there was no-one there, they passed through it and walked up the stairway on the other side. Reaching the top of the stairs, they stepped out onto a balcony, noticing a figure standing in front of them, leaning over the balcony railing, observing the village.

"Greetings Itachi, I see you've decided to join us after all." The man spoke. Itachi replied with a swift "Hai".

"But it seems you've brought someone unexpected." He said.

"Hey!" Naruto shouted out, only for Itachi to grab his shoulder, turning him around to face him and shaking his head, Naruto soon quietened down.

"He will be a powerful ally; that I can assure you." Itachi replied.

"Yes, I can sense that boy's chakra; it's stronger than any I've ever felt before, even my own." He continued whilst still looking out across the village. "But have you ever felt pain before? Do you know what it's like to feel like the whole world is against you, having everything you've ever loved brutally torn away from you, in front of your very eyes?" He asked. This time he turned around. "Do you know what it's like t-". He stopped dead as he opened his eyes and caught sight of Naruto.

"...What? This cannot be." He spoke quietly.

"Hey, your eyes look like mine!" Naruto shouted.

'This boy, his eyes are the same as mine, yet he possesses almost twice my chakra, this is impossible, yet I'm staring right at him.' Nagato thought to himself.

"What is your name boy?" He asked him.

"Uzumaki Naruto." Naruto replied.

"I see." He thought about what he was about to say for a moment, "Very well, Konan, take him to an empty room, I shall be along once I've conversed with Itachi." He said.

Konan merely nodded while gesturing for Naruto to follow her.

Itachi nodded once before speaking. "You should know something else; he's the Jinchuuriki of the Kyuubi." This caused Pain to freeze before turning to Itachi, gesturing for him to continue, "But as I'm sure you've noticed his chakra pathways haven't adapted to the Kyuubi's chakra, it seems to me, that the Rinnegan has suppressed it's influence. You could theoretically remove the Kyuubi from him, without killing him in the process as his body doesn't rely on it." Itachi continued. "As for pain, he was beaten daily in Konoha, his apartment needlessly vandalized, there were a select few who appreciated him, I'm sure you know of them. It was Sarutobi Hiruzen, Hatake Kakashi and Jiraiya. The rest of the village is most likely celebrating his departure." Itachi finished.

"I...see" Pain replied. "He will be a fine ninja, I will have to oversee his training here though, the Rinnegan will crush him if he's not prepared for it. I shall introduce him and yourself to the rest of the members tomorrow; I have a plan that will require all of you." He stopped, seemingly thinking. He turned back to face Itachi before continuing.

"Now, I'm sure you'd like to get some rest from your journey, Konoha will never think to look here, so you're safe for the time being." Pain spoke, Itachi merely nodded before following him out of the room; they soon reached a door. "You can stay in here for now." He said, before walking off, leaving Itachi outside the room.

Naruto was currently sitting on his bed, bouncing up and down, with Konan standing by the door, watching him. The door opened and Pain stepped through. He glanced at Konan, before stepping in the room fully, and speaking to Naruto. "Naruto, I would like to speak to you about something, it's important." He told him.

"Alright" Naruto answered, stopping his bouncing and sitting the bed properly.

"So be it. I'm going to tell you about those eyes of yours, as Itachi has most likely already told you, they are called the Rinnegan, and were possessed by the so-called God of Shinobi, The Rikudou Sennin." Naruto merely nodded, before Pain continued. "What he most likely didn't tell you are the benefits of having such eyes; first, you possess all six of the Chakra elements, allowing you to perform almost any technique you wish. Second, they provide you with a huge amount of chakra just by awakening them; I won't ask what happened to cause this. However, it seems you had a huge amount of chakra to begin with, so your levels are now the highest I have ever seen." Naruto sat there in silence, taking it all in. "There's something I want to ask you; before you awakened the Rinnegan, did you have any other episodes? Fits of rage where you'd black out and wake up, not being able to remember what had happened?."

Naruto shook his head; "No, this is the first time it's ever happened."

'I see, Itachi was right, there's no trace of the Kyuubi's chakra at all, even on his stomach, where the seal of Jinchuuriki usually is. We may be able to take remove it from him without killing him. It'd be a tremendous waste if he were to die.' Nagato thought.

"I also know you're the container of the Kyuubi." This caused Naruto to visibly flinch. "However, we may be able to remove it from you, normally this would kill you, but it seems like the Rinnegan has suppressed it's influence from birth, therefore your body has not become accustomed to it's chakra, so it's just sitting there inside you. Almost separate from you." Pain finished.

Naruto sat there for a moment, he looked down at his hands and clenched his fits. He nodded to himself before glancing back up and saying:, "I'd like to risk it, I just want to be seen as me."

"I understand, tomorrow I will introduce you to the rest of Akatsuki and we shall begin the sealing from there."

They both nodded, before Naruto could open his mouth, Pain had already begun answering his question. "Your training Naruto, will consist of me teaching you the various techniques of the Rinnegan, however, I will only teach them to you once I see you can handle them. I'll have the rest of Akatsuki teach you as many elemental techniques as possible, we'll also discuss Taijutsu but all of this will come later. For now, I'm sure you'd like to rest. Come Konan."

Naruto merely nodded before Pain and Konan left the room, leaving him alone, Naruto merely laid back on his bed before saying to himself:

"Well, that was some birthday."