Alright, here is the redone, new version of Project X! Now, I have had the problem of year measurement. So, after much thinking, this is how it'll be: since the myth of chakra is mostly of Rikudo Sennin, we will be measuring the time by that. Kyuubi attacked c. October 13, 2127 A.C. (After Chakra - which is when Hagaromo and Hamura defeat the Juubi) Program X was made two years before, and Naruto was born three days before.

Program X

Chapter One - The Project

He lived in the orphanage since he could remember. As an orphan with no knowledge of his parents, only told they never wanted him. The Hokage explained to him that his parents were loyal ninjas to the village at one time - but they died. He was confused whenever he asked for the names of his parents - like any orphan that didn't know their parents - but he was denied knowing anything about it. The only thing that was told to him was what they once were and what they did. He was too young to understand at that time there was something more.

Naruto grew up in the orphanage but was taught differently than everyone else. He was disciplined more. For example, instead of spankings - he was whipped. The leather of the whip was frayed at the end which left deep marks on his back. It would bleed for a long time. He would be fixed up by the nurse, who was the only nice staff member that worked there. His scars stuck with him; to remind him of the abuse.

It was when he entered the Academy that he left the orphanage and got his own house. Of course, he wouldn't have left if it wasn't for Hiruzen's help. The old man paid for the house each month and gave him an allowance for groceries. But even more problems arose. Stores wouldn't sell to him and the Civilian Council denied any form of complaint he tried to file.

This didn't mean his life was hard. People took it personal when the Demon entered the Academy for Ninjas. It started as simple glares and whispers, but on his birthday - the celebration of the death of Kyuubi - he was attacked by a group of older men. They were between the ages of twenty to thirty years old. The men were shinobi, you could tell by the way they fought which showed their training. They also disguised themselves as civilians and that is one of the shinobi ways, too.

He was saved by a passing patrol of Konoha's Police Force, the Uchiha. They are the only clan with the Hyuuga that made any attempt for Naruto's life to be better. It was Mikoto Uchiha, the Clan Head's wife, that filed for adoptions multiple times even when it was turned down by the Civilian Council. This only made it a clan effort to do everything in their power to protect Naruto.

When it is brought up at the Konoha Council that stores were denying Naruto their sales, Fugaku Uchiha, the Clan Head and operator of the police, made a huge raid on the stores. It was a bold risk, if anyone looked back at it, since he was bending many laws that were in place. Luckily, it was found that his reasons were sound, but only because he found an old law back during the time of the founding of the village.

He explained that it is illegal to deny sales, or unfairly charge anyone because of their background or past circumstances. When he added that everyone denied him because of his demon alone, it was hard for the Civilian Council to excuse their actions. But even with now being allowed to shop in the stores, Naruto wouldn't buy from them and instead went to Ichiraku all the time.

Now, I remember I was turning eight. I live in a three-bedroom and two-bathroom house that was my birthday present that year before. It was paid off by the Uchiha since I don't have close to enough money to pay for the taxes. I made few friends, mostly with Sasuke Uchiha and Neji Hyuuga, but I was fine with that.

But this story wouldn't be told if everything was so hunky-dory. My life changed on the night of my eighth birthday. I should thank those assholes, though. Maybe next time.

(O.O) Naruto's House - 19:30 (O.O)

A young blonde, one Naruto Uzumaki, sat on a black sofa in the living room while watching the television. Currently, he was watching a stand-up comedian at the Daimyo's son's anniversary party. Everyone was laughing at the man's jokes, and the Daimyo was even in tears because he was laughing so hard.

Knock! Knock! Knock!

Naruto paused the television, turning to look at his door in confusion. He looked through the window's blinds and caught a glimpse of Sasuke and Neji. He grinned and hopped off the couch, running to the door as soon as his feet hit the floor. He swung the door open and grinned at the two brunettes. "You guys made it!"

The two males grinned, not like their normal selves Naruto noticed. "Are you okay?"

"Fantastic," the two replied as Neji moved from the door to allow other strangers in and this is when Sasuke grabbed Naruto by his neck.

"Ack!" Naruto choked as he gripped the hand that held his neck. "Who are you?"

The two chuckled before they dispelled their jutsu. Sasuke grew a foot taller, his body bulked twice his normal size, and his hair brightened to a sandy brown. His left eye was brown and his right eye was green. Neji also grew an inch shorter than her companion, and her hair was a bright pink. Neji's green eyes twinkled as she grinned at Naruto maliciously.

"We finally got into the Demon's lair." She spoke before attending to the men who trashed the house. They knocked down pictures, smashed the TV, spray-painted the walls with vulgar words, and ripped and destroyed all of the furniture.

"Bring him over, honey." The pinkette spoke from the kitchen, and the man holding Naruto immediately followed the order.

Naruto's eyes widened when he saw a makeshift fire in the ground under his floorboards, made from his chairs, tables and pictures. He saw the large pot, big enough for a grown man to fit in, with boiling oil filled to the top. "They wouldn't," Naruto's mind screamed!

"Bring him here." Pinkette barked, while grabbing a ladle and dipping it in the bubbling oil..

Naruto struggled as he was put on his feet and forced to face the pink-haired woman. She pulled out the ladle and grabbed Naruto's arm, digging her pink-polished nails into his skin. She brought the ladle over a part of his arm and grinned with such venom before pouring the burning oil on his arm.

"Aaahhh!" Naruto screamed as he thrashed around, kicking his leg into the shin of the torturing woman.

She scowled at his useless attempts before grabbing his hair, pulling it to the side, and scooping up more of the liquid. She brought it over his face before dropping it. She poured four more ladlefuls before feeling satisfied with the bruised and red state she left his face in. His eyes were forced close and he lost all feeling to it, which was evident when he didn't even register when the woman slapped his face.

"Toss him in." He heard her say before being pushed forward.

(O.O) Council Room - 20:01 (O.O)

Hiruzen sighed as he mindlessly listened to his old teammate, Koharu Utatane, talk about complaints from civilians living next to Naruto. There were many, no doubt about it, but that didn't make them any more ridiculous. It went from him mowing his lawn to having his windows open on a hot day.

Most of the Ninja Council were annoyed at this repetitive topic. The most visibly annoyed were Fugaku Uchiha and Hiashi Uchiha. The two were next to each other, their arms crossed over their chest and scowls on their face.

"You'd think this would get old after a while." Fugaku spoke, his dark eyes eyes narrowing as he felt a chill dance up and down his spine. "Wait, do we have anyone watching Naruto?"

Hiashi raised an eyebrow. "I would think so. Hiruzen says that he have one of his personal Anbu watching."

"And you trust these Anbu?" Fugaku questioned, knowing that those that held a grudge against Naruto were usually the older and more experienced.

"It said it was Kakashi." Hiashi assured, though as he thought about it Kakashi never knew the true death and heir of Minato and Kushina. All he knew was that Naruto had the Biju, and that the man that he held closest to a father died in the attack by that very Biju.

"Exactly," Fugaku replied when he saw Hiashi's features change. He pushed him out of his chair was was about to leave when the door burst open by a young Chunin.

"What is the meaning of this?" Hiruzen demanded as he looked at the Chunin. "We are in the middle of a meeting!"

"We got a disturbance call from Naruto's neighbors." The young man replied, shrinking at the old Hokage's gaze. "They say they hear hysteric screaming."

Hiashi abruptly stood up and settled his look on the Chunin as Fugaku pushed his way through the lane. "And when were they sent in first?"

"Er," The young boy scratched his head in guilt and embarrassment. "The first disturbance call came in about twenty minutes ago but we chalked it up to a ridiculous reason. It was five minutes ago that we got multiple calls coming in with the same thing."

"What about that Anbu, Hiruzen?" Fugaku shouted as he slammed the door open and stormed down the halls.

Danzo stood up, hobbling through the lanes with a blank face. "Wolverine, you and your team head to the Uzumaki's building. Now."

A shadow from behind Hiruzen shifted slightly as a part of it moved out the window, followed by two more, and Tsume stood up to follow Danzo. The room was left in puzzlement, some of the civilians sweating with the knowledge of what was going on. And their involvement in some shape or another, like paying off that Anbu.

(O.O) Naruto's House - 20:05 (O.O)

Naruto laid, disfigured as boils were left on his once-unblemished skin and he shivered in pain as it hurt to just lay on the floor. Over him stood the large man and pinkette woman. They were smirking, the mob of assailants gone once they made the house look like a break-in and robbery. The pot of oil was nearly gone, about two gallons left at the bottom, and the ladle in the woman's hand.

"Why?" Naruto sobbed, his salty tears stinging his scarred face as he looked up at the two with bloodshot eyes. His once luminescent blue eyes were a dull grey, and the red around his eyes made him look even more scary - even demonic if the word wasn't reserved for those in Hell.

"You want to know why?" The pinkette sneered as she crouched down, grabbing Naruto's face harshly while he whined at the grip. "You attacked this village eight years ago unprovoked, Demon! Many died protecting this village. Husbands, wives, sons, and daughters! Even my son! You killed him!"

Naruto was left speechless as he looked into the woman's tearful eyes. Her green eyes looked sorrowful and the man behind her looked down in sadness. His hands clenched in slight anger but he didn't do anything.

"I'm sorry for your loss." Naruto whispered, but yelped when the grip tightened on his face.

"You want to know the hardest thing for a mother to have happen other than their child dying?" She questioned, her eyes glaring in anger as her tears stained her face with her make-up. "Not being able to have a body to say goodbye to and bury him with the honor he deserves! You incinerated his body with your foul chakra! But not now!"

She yelled, grabbing the kunai she had hidden under his dress. "This time, I will avenge him and all of those that died at your hands! They will all be able to move on in peace at your death!"

Naruto closed his eyes, ignoring the movement of the woman raising her arm, and waited for the kunai to kill him. I'm sorry.

When nothing happened, he opened his eyes to see the woman's eyes wide. Three bones were sticking out of her chest, and the man behind her was beheaded, his head ripped from the rest of his body by someone behind.

"Is he alive?" Naruto heard, his mind fogging as he was released by the woman and collided with the wooden floorboards. He weakly looked at the face that lowered to the floor. The skin was pale, their eyes black.

"He's awake, but barely. Let's get him out of here." The man spoke, his voice startling Naruto's eyes open, but only for a second.

"Itachi," Naruto whispered the name, falling into a world of bliss.

The man sat up straight, his black wings shifting slight at the name. Was his ears deceiving him? Did Naruto just speak his name? "I must have heard it wrong."

"You didn't." The man with bones out between his knuckles, his grey and black outfit daunting in the night with red eyes. "He recognised your voice."

Itachi narrowed his eyes but stood up, taking the young boy into his arms carefully. He turned around and walked out the building. "I'll meet you at the base."

A third man appeared just as Itachi flew off into the sky with his wings. He wore a black suit with grey lines, a red belt buckle with a black X on his waist. Orange glass on his head, only his nose and mouth showing out of the black suit.

"Is Naruto alright, Shisui?" The man asked, turning to his companion next to him.

"Just barely." The man, now named as Shisui, replied. His bones retracted into his hand before walking off. "Let's get back to the base."

(O.O) Hidden ROOT Base - 21:54 (O.O)

Hiruzen looked through the glass as doctors and surgeons worked on Naruto's scarred skin. Danzo was next to him, his eye closed while silently thinking to himself. The two hadn't talked to each other since Naruto was brought in by Itachi. While Hiruzen was worried over Naruto, Danzo was quiet and otherwise calm of the situation.

"I want him to be in the Program." Danzo finally spoke, opening his eye to look at Naruto.

"No," Hiruzen cut in as soon as the words left Danzo's mouth. "He needs time to...heal."

"And who will protect him during these healing periods, Sarutobi?" Danzo pushed, turning to face the man. "We know this won't be the end. Naruto needs more than that stunted Academy teaching. Let me take him. I'll have him watched twenty-four seven."

"I said no!" Hiruzen yelled, his voice rising to a high, deep level as he looked at Danzo. "He will not become one of your little puppets! You're lucky that I'm not putting you in jail for still having ROOT!"

Danzo's features softened before reaching into his shirt and pulled out a portfolio. He handed it to Hiruzen, who looked at him puzzled, but took the folder and opened it. Inside is, in bold words, something called "Program X." As he read it, he was becoming more and more shocked.

"Project X, created in June 5, 2125, was born from the ROOT program. It was a side project created by lead scientist Akane Inoue to enhance and make new abilities for future ninja generations. On October 13, 2127, the attack from the Kyuubi greatly diminished the ability to produce a working pill beyond the abilities of the Soldier Pill. But with the assurance and leadership of Akane Inoue, the research kept progressing. The ingredients for the pill were not working, and with the approval of Danzo Shimura, Akane Inoue was tasked with finding a new way to make it.

She traveled to the Unknown Countries across the ocean far past the Kiri islands. There, she consulted with many of the local tribes that accepted her and only two had powers far different than chakra. They mixed and strained native herbs and roots and gave it to the boys that would come of age in a great ceremony. When the two tribes came together for the ceremony, Ra's Al Ghul, leader and strongest warrior of the combined tribes, gave her own cup of the liquid since they saw her as a trustworthy woman, and to say she was surprised the next few hours is an understatement.

The next day, she was able to control the shadows around her and fly - though more like stumble through the air. She spent three days with many of the tribals' best teachers, practicing her skills the best she could. She returned with a young man named Kano, who Ra's Al Ghul taught, and plenty of herbs and roots for the medicine. Since January 1, 2130, there have only been five people "transformed": Akane Inoue, Shisui Uchiha, Itachi Uchiha, Hizashi Hyuuga, and Tsume Inuzuka."

Hiruzen looked the paper over a few times before shakily grabbing for a chair behind him and slowly sat in it. "You mean to tell me you went behind my back, without my permission, and contacted an advanced tribe beyond any charted land, and made your own soldiers with powers far beyond chakra?"

Danzo nodded, sitting down next to the old Hokage. "A side effect is that all ability to use chakra is suddenly stripped away and replaced with their new abilities."

The two were quiet, Danzo watching Hiruzen closely though the Hokage had his eyes in the palm of his hand. Slowly, he looked from his palm to Danzo, his stare cold and sharp. "What will you do with this discovery?"

"With your permission, I will start with a small group of young children and train them to be different - stronger - than any ninja would be their age. If they look promising, I will create a taskforce of them and have them do missions that are too sensitive for public eyes." Danzo stopped, looking at his lap before continuing. "Naruto Uzumaki has always been my first choice, along with Sasuke Uchiha since the two get along very well. Hizashi has already given me permission to do the same with his daughter, Neji, for the past few months now."

"Is there a hidden agenda behind you doing this?" Hiruzen declared, his tone still suspicious.

"Other than protect the village and world I love, not really, no." Danzo spoke before standing up and walked to the window. When he looked in, he saw the doctors finishing their work. "Come on, let's go see the doctor's report."

I hope this comes out as good as the original if not better. Anyways, comment your thoughts on how it is and what can be done with it. R&R!