I don't own Naruto or TMNT
This will be a slight age difference where instead of graduating the academy at 12 they graduate at 14 instead.
In the forest of death, a 6 year old Naruto Uzumaki was laying in a pool of his own blood after being attacked and left for dead by Villagers and a few ninja of his home village of Konoha.
A figure slowly approached the body of the young boy and picked him up before disappearing.
When Naruto awoke he found himself inside a tunnel of sorts and he looked around and saw old furniture and torches on the wall and thought "where am I and how did I get here."
He slowly got up and winced in pain as he looked at his chest and saw that he had been bandaged and he said "Hello." as he realized someone had to have bandaged him.
An old voice said "Hello young one." as Naruto looked and saw a figure sitting at a small table with a robe covering himself up and drinking something though Naruto could not see who the person was.
Naruto asked "Who are you."
The figure said "Who am I, hmm.....now that is an interesting question. First tell me, why were you in such bad shape when I found you."
Naruto eyes darkened and said "I was attacked by some stupid villagers and I don't know why. They kept screaming demon and making me pay."
The figure said "I see. To think humanity shows such cruelness to their own even in this day and age. Come, join me for some tea." as he motioned with his covered arm toward the seat across from him.
Naruto slowly walked over and sat down and asked "Where are we and who are you."
The figure said "My name is not important young Naruto but this is my home."
Naruto asked "How do you know my name."
The figure laughed a little and said "It was written on your cloths when I bandaged you."
Naruto took the cup of tea and said "Oh." as he sipped it.
The figure said "Tell me Naruto, what do you plan for your life." as Naruto tried to look at the figure but the hood of the cloak was covering his face so he couldn't see.
Naruto blinked and said "I want to be Hokage just like jiji so that way people will quit attacking me and giving me those hateful looks and respect me."
The figure said "Hokage huh........so you wish to be a ninja."
Naruto nods and the figure said "I am a ninja, not like those people in the village you come from who has those flashy jutsu but a true ninja, trained in the ancient arts of deception and stealth, a true silent assassin."
Naruto asked "What do you mean."
The figure said "I mean that what you call a ninja in this day and age is nothing more then a common thug compared to what a true ninja is. In my days my brothers and I were masters of the shadows, legends that struck fear into the heart of our enemies and brought hope to those who were being hurt by those who would harm them. Just the mention of our name was enough to make the bad guys run scared."
Naruto said "Then you famous like the Yellow flash or something."
The figure chuckled and said "Something like that. You see, my story goes to another time and place. Where science and technology was the mainstream of the world and where a pizza could be delivered in 30 minutes or less."
Naruto blinked and said "Huh."
The figure laughed and said "Perhaps I should tell you my story. For you can call me Master and this is the story of the Teenage Mutant Ninja Turtles and their fight against the evil Shredder and the FOOT clan......"
Several hours later the Sandiame Hokage was walking toward his home late at night tired from a hard day in the office and he was passing by an ally when a voice said "Pardon me Hokage-sama but may I have a word with you." making the third stop and look around.
He looks at the ally where a shadow of a person could be seen and the third slowly walks toward the ally after looking around and discreetly pulling a kunai out of his robes.
When he is a few feet away he asked "What is it."
The figure in the ally said "I have information on someone who calls you jiji."
The thirds eyes got wide and he started to say something when the figure said "he is safe. I rescued him after some villagers and ninja attacked him and left him for dead."
The third asked "Where is he." as he glanced around.
The figure said "He is in my home resting at the moment. If you would like to see him you will have to follow me alone."
The third asked "Why."
The figure said "Because I do not trust your people. I mean the boy had 3 broke ribs, several kunai and shuriken wounds and severe bruising when I found him."
The third said "I take it your not from this village."
The figure snorts and said "Thats an understatement, now if you would like to see him then follow me. If not then you will never find him." as the figure turned and took a step and fell into a sewer drain making the third blink.
A voice said "Come on if you want to see him because I won't wait for you." as footsteps could be heard leading away and the third frowned and stepped down into the sewer and he began to follow the figure.
About 20 minutes later the third came to an old wooden door that was open and he could see torch lights and he stepped inside and saw Naruto asleep on a couch and he saw the figure go over and sat a tea pot on a small fire and the third went over and checked on Naruto and saw he was sleeping and the figure said "I gave him some herbs to make him sleep until morning since hes still injured to give him time to recover. He heals increasingly fast."
The third frowned and said "That he does, now who are you."
The tea began to whistle and the figure took it off the fire and said "Join me for some tea and we can talk all you would like." as he poured himself some tea and the third sat down and after waiting for the figure to take some he took a sip and the figure said "You can call me Raphael."
The third said "Very well Raphael, now would you mind telling me what is it you want."
Raphael said "The boy talks very highly of you. In fact he wants to be just like you when he gets older."
The third said "Yes, hes told me this on several occasions." as he took some more tea.
Raphael said "The boys father never meant for his life to be this way."
The third stiffened and Raphael said "Relax, I owe Minato my life after my brothers and I first arrived here many years ago and I would never do anything to betray the debt I owe him."
The third asked "What do you mean."
Raphael sighed and said "Please do not freak out when I remove my cloak. It will make things easier to explain if you can see proof."
The third watched as Raphael took off his cloak and went wide eyed and Raphael said "You see, my brothers and I were originally normal pet turtles until an accident with a chemical known as the ooze changed us to what you see me now. My master Splinter who was originally a pet rat of an ancient master of the ninja arts learned the true ancient arts of being a ninja from his cage and then after he met with the ooze he also changed into a humanoid Rat. He then trained my brothers and I and we went out and saved the world from the man who murdered Splinters master and his clan. During our many battles with Shredder and the Foot clan an ancient artifact that allowed a person to travel through time was discovered. Shredder was able to use it to travel to this time line here around I would say 10 years ago and my brothers and I followed him here. We fought him in what you know as the forest of death and after the battle my brothers were all 3 dead as was the shredder. I was wounded and would have died but Minato and a woman named Kushina came across the scene of our battle and they saved my life. My brothers bodies were buried where they fell and the shredders body was destroyed but I have his armor over there." and the third looked where he was pointing and saw the armor.
Raphael said "Now as I was saying, after that I returned to my own time to be with my friends but I have returned several times to be close to my brothers. In fact I was paying my respect to them when I came across the body of Naruto in the woods and brought him here having realized who he really was by just looking at him."
The third said "What is it you are getting at because I can tell you did not just bring me here to here all this."
Raphael said "You are wise as they said but what I wanted to ask was would you allow me to train the boy in the true art of a ninja. I do not know your ways of chakra but I am a master of stealth, hand to hand combat, weapons, and discipline. I don't know why he is hated here but no child should have to live with this unless he be destroyed by it. I can take him away from the hate....at least until he is strong enough to take care of himself."
The third frowned and said "You wish to take him back to your time, don't you."
Raphael nods and said "Yes, there I can train him as I was trained so that way he can be a true ninja."
The third asked "And what of the need to use chakra. You said it yourself that you do not know how to use it."
Raphael said "I may not but....I do know someone who can."
The third asked "And who would that be."
Raphael said "A girl named Rin who was a student of Minato."
The third was wide eyed and Raphael said "She had discovered me one time when I was here visiting my brothers and she asked to leave this place because of the painful memories. I accepted after she told Minato and he approved it and so she lives in my time line now."
The third said "I see." as he heard whimpering and he looked over at Naruto who was shaking and both heard whispers of "please stop...don't hurt me....I'm no demon..." and the third looked down and thought "what has this village done to him."
He looked up and asked "How long will he be gone."
Raphael said "It will depend on him. I would say no more then 10 years though."
The third said "When do you plan to leave."
Raphael said "Tomorrow."
The third said "Very well, he may go with you but I want to see him off and also allow me to gather some scrolls and books to help him in his studies. Rin's been gone for a long time now and she may have forgotten some things."
Raphael said "Very well. I shall take you back to where we arrived and you can meet me in the manhole tomorrow at dark and we will leave then."