The ages will be set back slightly. I feel that having someone become a ninja at the age of twelve is a little to early. In this story Naruto will graduate around the age of 15 so everyone will be getting a boost in the age department.
Souls
Prolog
A short young blonde sprinted around the corner. He grinned with his latest achievement of letting the Inuzuka dogs loose into the village. As he ran his navy blue shirt ruffled in the wind. His vibrant orange pants doing the same. Both articles of clothing were much to big for him, but it was all he had, not that he minded.
As he rounded another corner he came into contact with something slightly hard and landed on his butt roughly. He looked up and saw someone he did not recognize. In a panic he quickly got up and tried to bolt for it.
His mind immediately went towards his previous prank and the coincidence of someone knocking him down. In a sudden stop the rest of his body besides in neck up continued forward slamming him into the ground.
He ground as he looked up and saw the person again. The man grinned at him as his black eyes changed into red.
"Hello little boy." He said with a sneer. "What do you think you are doing?"
"Nothin. I wasn't doin nothin!" Naruto shouted in response.
The man grinned even more if that was possible and picked Naruto up by the back of his shirt and carried him into a near by alley. As he approached the back of an alley Naruto spotted a hole in the ground.
He already knew what the hole was used for. Sewage access. He had used the tunnels many times to escape after a prank. Nobody thought to check them, so it was basically his own little secret. As he thought about the sewage system he yelp as he was shoved down the hole and fell on his back once again. The man jumped down after him and slid the cover back in place blocking out what little sunlight could enter the hole.
The dim lights that lined the walls gave only enough light to show that the man was still grinning from ear to ear.
"Do you know who I am little boy?" The man asked.
"N-no." Naruto stuttered out.
"My name is Shisui Uchiha." the man replied. "And do you know where I brought you down here?"
"No." Naruto replied steadily this time.
Shisui grabbed Naruto by the neck and replied in a low voice. "I am here to torture and kill you on behalf of the Uchiha clan." With a quick movement he made a kunai appear and slammed it into Naruto's hand pinning it to the wall.
Naruto screamed in pain as blood splatted the dirty floor. He gritted his teach and managed one word. "Why?"
"Why?" Shisui asked in an assumed tone. "Because you have the Kyubi inside of you of course." The man began cackling and slammed a kunai into Naruto's other arm pinning him to the wall.
Naruto cried out in pain again as he hung from his hands. The blades of the kunai slowly cutting into his hands threatening to slice them in half if not for the bones. No more words were said from the man as he began placing more kunai into Naruto's body attempting to kill him ever so slowly.
As the man ran out of kunai he grabbed the tanto that was on his back and removed it from its scabbard. With a grin the placed the tip of the blade against Naruto's skin right about where his heart was.
Naruto's barely conscious body fought fiercely against the kunai that pinned him to the wall, but there was no use. "Good bye." was all he heard as the tip of the blade pierce his skin.
As Naruto's passed out an explosion of red chakra burst from his body pushing Shisui back several feet. With a panicked look Shisui charged at Naruto intending to finish it. Suddenly Naruto's hand ripped forward leaving the kunai still embedded in the wall.
"Good bye human." Naruto said in a deep malevolent voice. His hand shot forward and stabbed into Shisui's chest just as he was about to stabbed Naruto.
"Tamashi Kyushu." Naruto muttered as the color from Shisui's body drained away. A dim purple flash of chakra ran up Naruto's arm and entered into his chest causing him to convulse. When that happened the rest of the kunai shot out of his body and embedded themselves into the wall across the tunnel.
Slowly a black ring formed around Naruto's iris as he slipped back into unconsciousness.
'It has begun.' a voice echoed inside of Naruto's confidence.