Thank you for finding my story and giving it a chance. There are some important changes that must be known before you begin the story.

First, in my story, Pain is actually the Deva Path with orange hair that was said to be the body of Yahiko. Search "Akatsuki Leader' or 'Pein' on Google images and you will know who I'm talking about.

Second, as an author I will do my best not to change the personalities of the characters created by Masashi Kishimoto. Writing anything short of that would be like creating an original character with the same name as Naruto. I will change many key and minor points around in the story, but I will keep all the non-original characters with their personalities. Let's begin.

(Note: This story is going to be huge and more than likely it will hold the longest chapters you will ever find. This isn't a warning as much as it a simple notice, depending on your preferences of reading. If you are interested in rather petite and somewhat unsatisfying stories, please continue your seach because that is not what you will find here. Also, Naruto will not be overpowered early on in this story, and he will have to earn his powers throughout the plot. This is not the story where he can match up evenly against Orochimaru in the Chunin Exams. Romance is carefully and realistically slow placed, and you won't find Naru-Hina until their relationship developes over time and in later chapters.)

Disclaimer: I do not own Naruto.

The Second Born

Chapter 1: The Path of Pain

The day had been long, and he was exhausted.

Nagato Namikaze looked below to what once was his village and closed his eyes as tears of sorrow fell down into the warm night. The large full moon that hung above him in the starry sky fully illuminated his face, reavealing the sorrow that it held. He felt the light and reassuring pressure of a hand fall upon his shoulder, and he didn't need to turn around to know who it was. He now openly wept until he was able to control himself.

"Today has been a day of suffering and loss," he declared in a voice filled with pain. "Konan, are you prepared to leave?"

He turned to his 19-year-old pure-blue haired female teammate and slowly ran his hand across her forehead looking at her pearly pupil-less eyes. Both of them were teenagers exposed to the cruel reality that is the life of a shinobi, and neither of them deserved what fate had bestowed upon them.

"Hai, I am prepared," she responded looking into the circles of his power filled eyes. The power of the Rinnegan.

"The seal is gone," he whispered in relief, now looking at her forehead with relief in his eyes. "There's no trace of chakra left…The removal was a success, and now you are free of that curse. Our mission… is almost complete."

Nagato turned once more to look upon his beloved village of Konoha. He sat down on the ground above the Hokage Monument as he thought of what still had to be done. The wind gently blew across his face as Konan sat next to him, wondering if there was a way to comfort him. He grieved for his father, for his mother, for the village, but most of all for his beloved brother. He had a duty as a shinobi of the leaf that he had to carry out, for the protection of all; his brother and the Shinobi world. His father had sacrificed his life for this village defeating the Kyuubi and he would be damned if seven years later it was destroyed by a coup d'etat. He closed his eyes as he thought of the last strong memories of his mother and of his father, the Yondaime Hokage.

Flash Back – 7 years ago

"Hokage-sama, it's been confirmed. The Kyuubi is headed for Konoha and will arrive in less than five days," stated a nervous messenger before the high chair of the Hokage's meeting room.

The Yondaime closed his eyes and placed his hands behind his head as he leaned back in his chair. All of the summoned Jonin, Anbu and Chunin present were standing before him silent as they waited for a response. A meeting as important and large as this one needed a room larger than the Hokage's office, so they gathered in another meeting room. Now, everyone was standing, waiting in fear. Fear of the Kyuubi, a demon only heard of in legends, which was surely coming to destroy their village. Even the most arrogant Uchiha present knew that his most powerful attack wouldn't even satisfy an itch of the Kyuubi. All hopeful and worried faces were upon their leader and only hope as he opened his eyes.

"Do not worry, for I have a plan," he spoke, loud enough for all to hear. "The Kyuubi is powerful; we all know this. There will be many fellow ninja who will die protecting the village."

Many ninja present quickly began to lose hope. If strongest shinobi in the world was unable to defeat the Kyuubi, then…

The strongest shinobi was not finished.

"But do not lose hope! He may take our lives, but there is no foe strong enough or no technique known that can extinguish our Will of Fire!" the Hokage shouting jumping up from his throne.

With such strong determination in his eyes, all were reminded why the 4th Hokage was claimed so powerful. Hope began to arise.

"There is nothing you can do for now. The burden of the Kyuubi is on my shoulders." the Hokage continued. "For now, go home and enjoy your family and loved ones; cherish your lives and those who you care about. Inform the population of my village of the Kyuubi, but give them hope! For we will be victorious! In three days time I will call a meeting of the entire village, speak of my plan, and then the children and mothers and citizens will be evacuated. The Kyuubi is a demon; he will care nothing of time and being punctual. He will have no problem arriving early. Hiruzen, stay after, we have much to talk about. You are all dismissed!"

Despite there being a door, all of the present ninja simply teleported away in seconds, leaving behind smoke and leaves. When it all cleared, the Sandaime remained in the meeting room.

Minato Namikaze, the Yondaime Hokage, dropped his emotional mask and began to weep while he told the Hokage of what he had planned.

A horrified Nagato Namikaze, son of the Yondaime, and soon to be a brother, left his hiding spot in the ceiling of the meeting room. He had successfully eavesdropped on this important meeting that was only for ninja of the Chunin rank or higher. He, though stronger than nearly all in the room, was still a Genin. He had always been praised as a prodigy, and had been training with his father since before he can remember. At age 7, he had activated his family's Kekkei Genkai, the bloodline limit, the Rinnegan. Now, nearly at age 13, he truly was a prodigy. One of the first lessons his father had been teaching him was chakra control, from how to walk on walls and water to masking your chakra from the normal senses of enemy shinobi.

Nagato had done just that as he listened in on how his father planned to defeat the Kyuubi.

His father's plan was logical; even the Sandaime, Hiruzen Sarutobi, agreed with it. His father was going to die sealing the Kyuubi within a young, preferably newborn baby. His little brother.

It was a logical plan, as the Yondaime had recently created this forbidden sealing jutsu, and he was the only one who knew how to use it. The Sandaime, in an effort to save his successor, would be furiously trying to learn the technique over the next five days, but he wouldn't be able to.

Of course he wouldn't. It was all logical.

But Nagato still hated it. He also hated crying, but that's what he did as he ran on top of the rooftops heading towards the Hokage monument.

His father, his Jonin sensei, would be dead in five days.

His dad had volunteered to be his Jonin sensei when it was time for Nagato to be a Genin, which was a year ago. His father had devoted his time to training his new Genin, while he left a special shadow clone in his office to do all of the 'boring stuff', as he put it. Nagato was considered even more of a prodigy than Itachi Uchiha, who was one year his junior, and he had been ready to be a Genin when most of the kids his age didn't even know what a kunai was yet. His father had always taught him that Shinobi ranking was just a formality, and that he should never underestimate his opponents, but he still had to make the rank of Genin the move up and complete harder missions.

So Nagato had been paired up with two other prodigies under the guidance of the Yondaime as their sensei, who had completed his duty as a sensei over Kakashi.

Life had been good then, but now his world was falling before him.

On the hill above the Hokage's monument, Nagato wept into the warm night, as he thought of the destruction to come to the village, and to his life.

End of Flashback

Nagato grimaced as he resurfaced from his memories. What had happened next became the worst day of his life.

Flash Back – 7 years ago

It was morning, and the peacefully village of Konoha was oddly silent, almost as if the birds themselves who found it their responsibility to fill the air with melodious chirping knew that the impending doom known as the Kyuubi was approaching. Nagato sat outside the hospital door where his mother lay soon to give birth to his brother. The Kyuubi was near. Everyone could feel it; the sinister chakra that seemed to be slowly creeping over Konoha. The nine-tailed demon fox would arrive today.

He thought of one of his teammates, Konan Hyuuga. She was sitting in the chair next to him, asleep; for she had fallen to slumber due to exhaustion on his shoulder. She had stayed in the hospital all of last night with him when his mother began giving birth. They had known that she was going to have baby very soon, and for the past two days she had been in the hospital.

Nagato had hoped that Naruto would be born late so he could avoid being used for the sealing. Nagato knew that it was selfish, but this was his brother! It was unfair that Naruto would have to become the Jinchuuriki of the Kyuubi!

His other teammate would have been there to support him but he was busy evacuating the population to a hidden part of the village and-

He was interrupted from is thoughts as his father opened the door of the emergency room.

"Father!" he yelled, "What's happened? Is Naruto born yet?" Nagato knew about Naruto's name because his parents had been talking about it for quite some time. After a short visit from Jiraiya who was announced as their Godfather, the name 'Naruto', which was the main character of his novel, was all but confirmed for the yet-to-be born child.

Minato Namikaze put his head down; tears were falling down from his face. The soon-to-be Hero of Konoha was breaking down.

"Father, what's wrong?" Nagato asked hesitantly, for he was not prepared to hear any more bad news.

Yet the news still came.

"S-She's…" Minato was clearly having difficulty saying this. "She's dying" he announced in no more than a whisper, as if he himself did not accept it.

Nagato sat back down with a shocked look on his face. Konan, who had been awake just in time to hear the news, broke down crying. She had no parents, nor could she remember them, and Nagato's parents were the closest family that came to mind. They easily welcomed her in, and they were so kind to her…

Minato gritted his teeth and continued. "She successfully gave birth to Naruto. B-b-but there w-was too much…too much blood. S-she's in surgery now but t-they said t-that…" He lowered his head again and wept.

"T-This wasn't supposed to happen. My son, Nagato, you weren't supposed to lose both of us… I'm sorry." Minato finished, looking at his son with is yellow Rinnegan activated.

Nagato was in too much shock to respond. No…this wasn't supposed to happen. Why? Why to our family?

Minato spoke. "The nurses will come out to tell you when she is ready to speak. I need to make sure Naruto is alright"

With that, he disappeared in a yellow flash, leaving Nagato and Konan to suffer alone.

Nagato entered in his mother's room along with Konan. There were three medic-nins running through clipboards, with a look of desperation and hopelessness on their faces. The two teammates saw Nagato's mother laying there on her deathbed, smiling at them when they entered.

"Nagato, Konan, how are you?" she asked in a jokingly manner. Even near her death she managed to keep her sense of humor. Nagato acted more like his father: reserved yet friendly, easy-going yet determined. Hopefully Naruto would grow with a sense of humor…

"M-Mother…I" he began.

"Shhh, I just wanted to say goodbye to my son and my daughter before I leave," she kindly explained with a peaceful expression on her face.

Konan was shocked to hear this. "Y-Your d-daughter?" she stuttered out to her.

She responded. "Yes sweetie. You have always been like a daughter to me and Minato-kun. And Nagato, you have always been a great child. Raising you was such a great experience. I…" Whatever she had to say was stopped as she began to cough.

One of the worried medic-nins quickly spoke up after hearing her cough. "Kushina-sama, you need to rest! You have no strength! You've lost so…"

"I know, geez, I'm a grown woman now!" she managed to giggle despite the pain.

Another medic-nin arrived through the door.

"The Hokage has arrived," he announced. He took one sad glance at Kushina before he left the room.

"Nagato, Konan," Kushina said to her young loved ones. "Good-bye. Always know that I loved both of you. And please… please watch over my Naruto-chan."

Nagato and Konan soon left with new tears in their eyes.


"My dear, he's so wonderful and energetic. And he looks just like me!" Minato told her with a sad tone in his voice. His first-born Nagato took a mixture of his parent' hair colors; Minato had shocking yellow hair, Kushina had pure red hair, and Nagato had bright orange hair. But Naruto had yellow hair and looked just like his father.

Kushina peacefully sighed as she cradled her second-born son against her chest. Suddenly, the will of fire came upon her and her motherly instincts consumed her logic.

"No!" she screamed. "I won't let you use him for the sealing! Not my son! I won't allow it!" she continued to yell at him.

Minato tried to explain to his now enraged wife what they had discussed before.

"Kushi-chan, you have to understand, I told you before that…"

"I change my mind!" she yelled again, tears of sadness streaming down her face. "Why does it have to be our family? There is so much happening to our family now…why can't you take another young child?" Kushina asked her lover.

Minato sighed. They had been over this before. He looked into the eyes of his lovely wife. The beautiful eyes that were once so full of energy were now almost lifeless and filled with sadness, which was all slowly fading away.

"How…How can I?" he quietly answered. "How can I ask another parent to sacrifice their child for the sealing? How can I look into the eyes of a mother and tell her to give me her child for the Kyuubi? How can I tell someone else to do a duty that even I am not able to perform?"

Kushina frowned. He had given her this speech before, though it sounded less worse when he had first told her. She coughed once more, feeling her own energy seep out of her with every breath. She could feel death coming upon her as she grew tired.

"M-Minato…I love you. I always have…" She told her husband, growing quiet.

He placed the sleeping baby aside in his crib, and he leaned in and gently kissed his wife.

"I've always loved you too Kushina..." Minato was holding back tears as he looked upon the love of his life.

Kushina closed her eyes and smiled as she rested her head in her pillow.

That night, the man who would sacrifice his son, kill himself in the process and lose everything had to watch his wife slowly die in his arms.

Outside of Konoha

The mighty Kyuubi in all his glory and rage began attacking Konoha. With his powerful nine tails swinging around, crushing mountains and uprooting trees, the demon was unstoppable. His evil chakra swept before the entire village, leaving a sense of horror in the memory of all. Children cried, and the citizens were frozen in fear gnashing their teeth.

All of the ninja Chunin rank and above were attacking the Kyuubi, doing all they could to hold it back. Anbu elites stood on the tree-tops casting powerful jutsus to the demon that was threatening their village.

Yet nothing was working.

Any hope of defeating this monster was lost the moment his presence was felt in full force. There was only one person that could possibly save them all now…

One Jonin of the village roughly landed against a tree as he was knocked back by the demon. Others who were beside him were clearly affected by fatigue and pain.

"Hold the attack and wait for the Fourth Hokage!" he shouted to he comrades. With that, he jumped back into the fight.

"Don't let it get any closer to the village!" another Jonin yelled out.

With that said, and explosion of destruction that rivaled the Kyuubi appeared next to the gathered shinobi. A giant toad with and equally giant sword and smoking pipe appeared on the battle field, with none other than the Fourth Hokage on top of it. To everyone, he was a sight for sore eyes.

On top of Gamabunta

He came for one purpose; to use one jutsu.

Minato closed his eyes as he prepared himself for what he had to. He had one last talk with his son Nagato before he had to leave for his duty. Nagato seemed to have accepted that Naruto was best suited for the sealing process.

Nagato believed that his little brother would be responsible enough to hold the Kyuubi as well. He also trusted that his father, who was the world's top first-class sealing master, would be able to create a seal strong enough that Naruto wouldn't even know that he contained the demon.

However, he disagreed when Minato claimed that he would be viewed as a hero. Surely the village would turn on the boy who held the Kyuubi.

Minato's last wish to Nagato was that he would protect and watch over Naruto.

"Naruto", he thought. "You deserve so much more than this. You deserve a full family. I'm sorry for what I have to do."

Minato smiled as he gathered the chakra needed to perform the sealing jutsu. Fighting the fox head on would only lead to his death, which the village couldn't afford, or it would lead to him no longer having enough chakra to use the sealing jutsu.

"Looks like this is it, Gamabunta, my old friend." the Hokage sadly called out to his summoning partner. Over the years the two had formed a powerful bond while working together.

"Damn it Minato! Why do you have to be the one to sacrifice yourself?" the giant toad complained. "You're a great ninja, and it was good working with you... I hope that I will meet one of your sons when they learn to summon me. Otherwise I'll be stuck with Jiraiya." the toad chuckled. "Farewell Minato…"


As if the Kyuubi could sense his own doom, he rushed to the toad in hopes of killing whatever was summoning such a powerful force.

But the demon was too late.

The Yondaime finished the necessary seals and in a brilliant flash a light, he activated the jutsu.

And the Kyuubi was no longer among the living.

Minato fell on his knees on top of Gamabunta, smiling at his accomplishment. He had saved the village. He smiled as he thought about his beautiful wife and their children, until he fell over, dead.

Hospital Room

A seal appeared on baby Naruto's stomach.

The Sandaime sighed. "It is finished." he announced to the medic-nins in the room as well as Nagato.

Nagato slumped down against the wall of the candle-lit room, grieving for the loss of his father, his mother and now for the Kyuubi being sealed within his brother.

His pain had begun.

End of Flashback

Nagato opened his eyes, Rinnegan activated. He turned and spoke to his teammate.

"Konan, where is he now?"

Sitting up straight, she formed a hand sign and concentrated for a minute before she responded.

"He's in the compound. We should probably go and see is he is alright."

Nagato nodded and stood up. "Let's go." he said reaching out his arm. Konan took hold of his arm and together they vanished in a bright orange flash.

The Uchiha Compound

Itachi Uchiha landed on top of a telephone pole with the moon behind him. His mission was emotionally destroying him. He closed his eyes as he remembered what the council had told him. Annihilate the entire Uchiha Clan, every one involved in their evil plan…

The words of the council and of the Sandaime still ran in his head. He was chosen for this because he could infiltrate the compound without suspicion and destroy it from the inside. Especially now with his new eyes, he was perfect for the job.

But that didn't mean that he had to enjoy it. The blood of his best friend Shisui and his girlfriend will forever be stained on his hands. And soon he would kill his parents, who were the ringleaders of the Uchiha Clan's plan of coup d'etat. Over the past few years he had grown farther away from his father; there was something off about that man. It wasn't hard to believe that as Clan Head he was in charge of the plans.

But his mother? She was always so kind to him, to everyone! He would have to interrogate as to whether or not she was a part of this foolish plan as well.

He would have to rest for a few minutes, as he had to use his Mangekyou Sharingan to kill the last group of the Uchiha Military Police Force that had formed a group and attacked him.

2 weeks ago

"Shisui, the plan," Itachi begged him. "Please tell me it's not true. Tell me you're against it!"

Shisui, his best friend since young, laughed evilly in his face. "Of course I am a part of plan." he responded. "Ever since I was young I have been raised on the plan to take over Konoha, kill the Namikaze's and the Hyuuga's, and how the blood of the Uchiha is the strongest in the world." He stopped and though for a moment. "I am curious as to why you never knew about it."

Itachi put his head down in pain. So it was true. The council and the Sandaime's suspicions were true. But he didn't understand, Shisui of all people…

"Shisui!" he yelled, aggravated now. "The idea of our blood being better is moronic! All of us should stop being lazy and strive for self perfection instead of relying on our 'Uchiha Blood'" Itachi said with disgust.

Shisui was frowning thoughtfully. "Our blood is strong, that's nothing to be ashamed of." he reasoned. "As a prodigy of our clan you should know this. I wonder why someone who doesn't even acknowledge his strength as an Uchiha would be so trusted among the clan. You are our undercover agent feeding us info. Unless…"

Shisui was now confused. A spy for the Uchiha clan should be one who believes in our ways. Instead he didn't seem to accept them, and he is asking him as if he was confirming it. Why did the elders not tell Itachi of the plan? Did they not trust him with such important information around the Hokage? It's almost as if…

Shisui reached a conclusion. "Don't tell me that you are double agent Itachi…"

Itachi looked up to his friend. "Yes, I am, and the Hokage has had suspicions of the Uchiha clan plotting to take over and…"

Shisui concluded for him. "I just confirmed it, didn't I?" He sighed and stood up. "Itachi, you and I may have always been best friends, but I will not let you leak this information out to the Hokage." he stated in his fighting stance, Sharingan activated.

Itachi was prepared. The Hokage had warned him that this might happen.

Shisui charged towards him.

"Then we will fight…" Itachi whispered to himself.

End of Flashback

Itachi had won the fight, at the cost of his best friend's life. He later made it look like Shisui had killed himself.

And now Itachi would have to finish the job with his parents. He looked at the moon behind him. It was starting to get late; he wondered where Sasuke was…

His thoughts were interrupted as an orange flash appeared in the compound on the roof next to him. When the flash disappeared, Nagato and Konan where standing on the roof.

"Itachi, have you finished?" Nagato asked out with sadness audible in his voice. He knew how hard it would be for Itachi to kill is clan.

Itachi turned to look at his teammates since young. "No, my family is still alive in the house." he replied with a perfect mask of emotions on his face. It would take years of experience as a shinobi to have such a blank mask on his face.

Nagato understood him. "Shall I do it for you?" he offered.

Itachi shook his head and disappeared in a burst of speed.

Minutes Later

Thump, Thump. His parent's bodies fell lifeless to the floor. Itachi stared at what he had just done with a mix of horror and cold fury in his eyes. Both of his parents had been the ringleaders of the clan.

He couldn't believe it.

He didn't have much time to think as he sensed his brother's chakra outside of the door

Right on cue, a 7-year-old Sasuke entered the room.

"Mother! Father!" he yelled, clearly exhausted from running around.

Itachi, hidden in the shadows, looked sadly upon his brother for what would be the last night in years. He walked forward to him.

"Brother?" Sasuke yelled in relief. If his brother was alive then… "Brother, Mother and Father are…" he couldn't complete his sentence. "Why?! How?!" he asked. "Who did this to…"

Swiissh Whatever Sasuke had to say was cut short as Itachi flung a shuriken at him. It was so fast, Sasuke couldn't even see it! He didn't even know what happened until a gash opened up in his shoulder.

Itachi stood still looking stone-faced at his brother, Sharingan still activated.

"Brother," Sasuke asked confused. "What are you..."

He was silenced by the emotionless glare Itachi was sending him.

"What are you doing brother?" Sasuke asked once more.

Itachi prepared his chakra for his Sharingan.

"Foolish little brother."

He closed his eyes to gather more chakra, and when he opened them Sasuke felt fear and terror freeze him.

"Mangekyou Sharingan!"


Nagato sighed and once more looked upon what was his village for a last time with his team. Itachi and Konan stood next to him

Itachi closed his eyes in frustration and exhaustion. What they had done was necessary. The mission would be complete as soon as they left Konoha.

The council had originally planned for Itachi to do the mission alone, but his team insisted, that if he was to become a missing nin, then they would go with him.

Konan agreed because she was tired of the Hyuuga clan and their ancient practices. After her part of the mission was complete, the Hyuuga clan would never accept her again.

Nagato had agreed because the Uchiha clan's betrayal to the Namikaze clan. He and Naruto were now the last two members. The Namikaze clan had always been praised for their skills, and they were soon to overcome the fame of the Uchiha.

The Uchiha, using their power as the Military Police Force had sent every Namikaze ninja frontline during the Kyuubi's attack, knowing that they would die in attempts to seal the power of the beast. The Namikaze's were a smaller that the Hyuuga and Uchiha Clans, but every member was a ninja. Nagato and Naruto were the only children in the entire clan.

But now they were gone because of the Uchiha's betrayal.

The Sandaime had ordered for the three to leave before sunrise, for he would begin to search for them in the morning. They would have to leave soon.

Suddenly, a new presence was behind them.

The three turned to look at the figure. He was wearing a black robe with red clouds on it. Akatsuki.

But what stuck out most from him was his orange mask with one hole for the right eye, with spiral patterns leading to that eye hole.

He goofily waved to them, as if he didn't notice the three's moods or as if they didn't know he was there. "Hey guys!" he practically yelled at them.

The three prodigies sighed at the man's antics.

"Sensei," they replied as one.

He turned around and began to walk away, and Konan and Itachi began to follow. Nagato stayed behind and looked directly at his 7-year-old little brother's apartment.

"I am sorry, Father and Mother, that I will not be able to watch over and protect him any longer," he thought to himself. "I must leave the village that has betrayed my family and my clan. My name is now Pain, and this is my path."

"But one day I will return to see how you have grown, Naruto."

He turned to catch up with the rest of the group. "It will be interesting to see how he grows out of the shadow of what I have done tonight," he continued to think. "I am no longer the legacy of the Yondaime. Today that has passed down to the second born, Naruto Namikaze."


A/N: That was hard to write. The start is slow, and not much else could be put in that was necessary to make this chapter longer. It was only the intro. The next chapters will hopefully be longer. For now this is the last part where I will be describing what is happening with Pain and his team. Naruto will appear next chapter.

Here are the ages as of now, if you were unable to catch them.

Nagato – 19

Konan – 19

Itachi – 18

Naruto – 7

Sasuke – 7

Yes, Konan in this story is a Hyuuga, and her powers, which are very different than that in the anime and manga, will be described later when I go back to their group.

Thanks for reading. Please review what you think of this story so far and how it will go.