Chapter 1: Secrets

Minato could be considered a genius. He was also considered to be one of the most powerful Shinobi in the five elemental Nations. The man had inspired fear and admiration during the Third Shinobi war and awe during his first day as Fourth Hokage. Minato's wife Kushina couldn't be more proud. That sissy she thought would be a weak shinobi turned the tables on them all. The village entered a relatively peaceful time during Yondaime's reign. That is until October 10th. The day Kushina and Minato's son would be born. It had been a terrible day. A joyful and sorrowful one. Minato and Kushina sacrificed everything to keep Naruto alive. Minato knew, that someday he would die. He knew it even before the Kyuubi attack. He knew that he had to take precautions in case that were to happen the moment Kushina told him she was pregnant.

So Minato, being the overprotective and slightly paranoid man he was…began a project. A secret project. The Yellow Flash researched and experimented. Spent countless hours creating his plan B. Using his own DNA, Minato created a clone that couldn't be dispelled. Made from his chakra as well as his own cells. His goal was to create a replacement for his future son in case of death. A replacement which would go to any and all lengths to keep the little boy inside his wife safe.

He knew if anyone found out, it would cause chaos, so he made sure to keep it under wraps from everyone. There had been one little problem however. The clone wasn't growing as fast as he originally predicted or wanted. After months of showing no signs of rapid growth, Minato decided to leave it be. The Yellow Flash took this dirty secret to his grave. It would stay that way for a long time…

Naruto was running. The little boy couldn't take the glares and insults he was being subjected to. 'Why do they hate me?' he asked himself. However, he had no answer for that. Naruto ran until he reached one of the abandoned training grounds. The forest was lush and mysterious and provided the perfect hiding place for the boy to cry his sorrows. The seven year old had recently been kicked out of the orphanage. The third Hokage had promised he would fix the situation soon.

'He better!' thought Naruto indignantly, 'I can't take one more day of this. Jiji better hurry ttebayo!'

Naruto walked aimlessly along the trees, looking around curiously. He hadn't been to this part of the village. Naruto made his way through the tree roots and grass until his foot touched something that wasn't dirt.

"Huh," Naruto hummed as he crouched on the ground. He knocked on the surface and was surprised to find that it was made of metal. He took some of the dirt, leaves, and roots out of the way. He made a face when he found that the ground looked exactly the same. Naruto looked around to see if there was anything else that looked suspicious. The blond couldn't find anything out of the ordinary. After hours of trying Naruto decided to go to sleep. He had no place to stay at the moment. He had spent two days on the street waiting for Sandaime-Jiji to fix something. Naruto leaned against a tree close to where the strange metal ground was. He was about to close his eyes when, suddenly, markings appeared behind him. Before the blond could see what they looked like, they disappeared.

Naruto shrugged and fell asleep.

The next day, Naruto decided to skip the academy all together. After all he had found something way more interesting. When the little ninja in training woke up the next morning, he found that the ground no longer looked the same as everything else. There was an entrance. Like one of the sewers around town. Naruto being the curious and hyperactive boy he was could not pass up this opportunity. The boy lifted the top off of the entrance and climbed down the ladder. The tunnel was standard, creepy and dark. There were arrows however. So Naruto followed the signs. At the end of the long hallway was a door. It looked rusted with a few coats of dust. Naruto slammed his body against the door a few times before it was knocked down.

"Ow man that really hurt…dattebayo…" Naruto panted.

The blond looked at the room he had uncovered. It was relatively normal. There was a table, some parchment, and scrolls. However, what made the room stand out was the giant test-tube. In that giant Test-tube was a very naked man. He was blond and slender. His skin was chalk white, from the lack of sunlight and his hair was long and unruly. If one were not careful and failed to notice his intimate parts, one would have assumed the man was a girl.

"Creepy much?" Naruto shuddered as he hesitantly stepped forward.

The boy reached the test-tube. Naruto touched the glass and a few markings appeared. The glass shattered, making Naruto stepped back a few feet to avoid getting hurt too badly. The contents of the tube came flooding out. Water of some sort. The unknown man dropped to the floor like a doll.

"Um…mister?" Naruto called.

The man moaned as his limbs twitched and his fingers moved involuntarily. Naruto carefully moved forward ignoring the slight sting from the scratches he had suffered from the shattering glass. He touched the man's shoulders and shook him.

"Hey mister! Wake up ttebayo!"

Cerulean eyes opened and met Naruto's. The man blinked a few times before sitting up. He touched Naruto's cheek and then his hair and stared into his eyes, with a deep, soulful, and analytical stare. Naruto felt like he was being picked apart. He was officially scared so he moved away. The man grabbed his arm and pulled him into a hug.

"You're my son," the man rasped, "Naruto. Naruto."

Naruto was officially stunned. What?!

"Hokage-sama!" Sandaime looked up from his paper work to find a frantic looking Iruka in front of him.

"Iruka-san," the old man acknowledge, "What troubles you? Is it Naruto-kun?"

"Yes!" replied the instructor, "he's not at school. He didn't show up today. I can't find him anywhere!"

The Third wasn't all that surprised. Naruto did ditch sometimes, however he was soon located. Regardless, Naruto was becoming stealthier by the day. Soon the Third feared the boy would give Chunins and ANBUs alike a run for their money.

"Alright, Iruka, let's calm down. I'm sure Naruto is fine. Go back to the academy. I will look for him myself."

Iruka seemed to be satisfied with that answer and shushined away. Sarutobi sighed and got up. He would have lecture Naruto again. He was slightly worried, but he was sure Naruto was in no danger. The old man got his crystal ball and watched.

Naruto ran. As soon as the strange test-tube man had said those words he took off running. He was currently hiding in an alleyway, hugging his hands and knees.

"That has to be the weirdest thing I've ever experienced in my short life ttebayo!" Naruto screamed.

Naruto watched as his scratches and cuts healed. He was unsure of what to do now. 'Maybe I can bother Sandaime-Jiji since it's too late for me to go to school…' Naruto stood up and ran to the Hokage's residence, ignoring the frigid glares he was receiving along the way.

"It looks like I won't have to look for him…" mused The Third.

The Test-tube man was left sitting there dumbly. He watched the boy run for the hills in fright. The man was hurt. But that didn't impede the man's reasoning. From the limited data he had, he gathered that his approach might have been too strange and slightly invasive. The man got up carefully and balanced himself before taking a few steps forward. All the man knew, was that he needed to take care of Naruto. Naruto was his son. He knew there was something else he was missing beneath the surface. More data he had yet to look through in his blank mind. However, That wasn't important to the blond man at the moment.

The Minato clone made his way through the dank tunnel and into the sunlight. He needed to find Naruto.

"Sandaime-Jiji!" Naruto stormed through the door, "When will I have a place to sleep?"

'Naruto-kun, I have arranged for an apartment to be assigned to you. It should be ready by tomorrow. There's no need to yell." Sarutobi blew a puff of smoke from his mouth. "Now, can you tell where you have been during the morning Naruto-kun?"

"I..well you see…" Naruto rambled looking away. He was a terrible liar.

Luckily he was saved by an ANBU at that moment.

"Hokage-sama," said the masked nin, "There is a naked man in the village sir."

Sarutobi Hiruzen wondered how long it would take for his heart to finally give way.

AN: Well another story idea. However, I feel bad about Making Minato do the creepy experiment like Orochimaru. It was fun though XD.