I don't own Naruto, Megaman and it's affiliates, or anything else that is crossovered with this. Spoilers if you haven't read the magna so if you don't want to know what happened in the future don't read.
NOTE Naruto is 2 years older then the rest of the Rookie 9 and a year older then team Gai. When the Chunnin exams start he will be 16, the same age as Temari.
Minato Namikaze was finishing the sealing of the Kyuubi with his wifes beside him with the Kyuubi tail stabing her before both died and the Kyuubi was sealed away. The Sandaime Hokage closed his eyes for a moment ignoring the crying Naruto in order to pay respect to Minato and Kushina for thier sacrifice and thought "I'll look after and protect your son for you both."
Just then the crying suddenly stopped and Hiruzen opened his eyes and blinked and looked at where Naruto had been and thought "What the...where is he." as he began to look around.
Several ninja appeared and the Sandaime who was looking around and said "Spread out and search the area for any survivors or anything suspicious. Especially a baby. This woman has recently given birth but I do not see her child." as he thought "Minato, where is your son at."
An ANBU with a dog mask moved beside Hiruzen and said in a low voice "Sandaime-sama, where's sensei son."
The Sandaime said "I don't know Inu, he was here moments ago when I closed my eyes to say a silent prayer and he vanished. He looks like his father, blond hair, blue eyes and 3 whisker marks on his face. Spread out and search for him but don't tell anyone what your looking for." in a quite voice.
Inu nods and jumps away.
Meanwhile with Naruto, a man in a white lab coat picked up Naruto and said "Don't worry Naruto, grandpa's going to take care of everything."
Time skip 8 years later
Anko Mitarashi was near the gates to the forest of death when an explosion inside the forest of death caught her attention and she thought "What the hell. Nobody is allowed in there." as she quickly jumped over the walls and entered the forest.
As she approached the area where the explosion came from she saw smoke and when she got to the source of the smoke she saw what looked like several 10 ft tall tigers were dead on the ground around a clearing and in the center of the clearing kneeling over the body of one of the tigers was a figure wearing a type of red, black, and gold armor with a black visor covering half the figures face making it where all you could see was from the bottom of the nose down to his chin with blond hair sticking out the back of the helmet going down his back.
The figure stood up before he turned to look at Anko and Anko said "Who are you and what are you doing here."
The figure turned his head slightly and spoke in a language Anko didn't recognise.
Anko looked confused and said "What did you say. I couldn't understand you."
The figure spoke in another language and Anko looked confused and the figure then said "Can you understand this." in a language Anko had heard years before.
Anko said "Yes, I can understand that language but just barely. Who are you."
The figure said in the same language as before "My name is Zero. I understand your language a little as it is an variation of Japanese though I would like to learn your language and culture. Who are you and is where am I."
Anko frowned and said "I am Anko Mitarashi and you are currently in the forest of death...but how did you get here."
Zero tilted his head to the side and said "Where are you from."
Anko said "I'm not the one answering questions. Either answer my questions or I'll take you back to the village to the Hokage."
Zero said "Village...Hokage...what is the name of your village and what is this Hokage...Is he the chief of the village or ruler there."
Anko thought "This guy must really be from far away. No wonder he speaks that language." and said "Yes, he is the leader of the Konoha."
Zero said "Then take me to this village and to this Hokage. Perhaps he maybe able to help me."
Anko frowned and said "Alright, this way." as she motioned and Zero began to head that way on the ground and Anko kept a watch on him. When the walls came into view Zero looked left and right looking for a gate and said "Is this village on the other side of this wall."
Anko said "Yes."
Zero said "How do you get on the other side. I do not see a gate."
Anko thought "How in the hell did this guy get in here in the first place." and said "There are gates but usually we go over the walls using Chakra."
Zero asked "Chakra. What is that."
Anko sweatdrop and said "Um...how did you get in here."
Zero frowned and ran at the walls quickly but before he got too close he jumped in the air and seem to be prepelled up into the air shocking Anko as she saw him clear the walls and she quickly ran and climbed the walls as she got to the other side she saw Zero looking around and Anko asked "How did you do that."
Zero asked "Do what." in a confused voice
Anko shook her head and said "Never mind, follow me."
20 minutes later Zero and Anko were walking through the village as several people got out of their way never seeing someone dressed like Zero was and several ANBU began to trail behind them.
As the Hokage tower got closer a team of ANBU appeared and one in an dog mask said "Who is this Anko and where are you taking him."
Anko said "He said his name is Zero and I found him in the forrest of death. He seems to be from another land as he speaks a language I haven't heard in years and I was taking him to see the Hokage in order to figure out what to do with him."
Zero asked "What's with the mask, are they reploids or mavericks." in the language only Anko recognised.
Anko blinked and asked "What do you mean by reploids and mavericks."
Zero frowned and looked around and said "Hmm...what are the mask for."
Anko growled and said "Damn it. Stop avoiding my questions."
Inu asked "What did he say Anko."
Anko said "He asked me what was with the mask, he wanted to know if they were reploids or mavericks. I don't know what either means."
Inu said "He understands our language."
Anko said "Somewhat. He claims it's a variation of a language called Japanese that he knows."
Inu frowned behind his mask and said "Lets take him to the Hokage."
Anko nods and said "Come on." as her and the 4 ANBU lead him into the Hokage tower and after knocking on the door into the Hokage office.
When the Sandaime Hokage looked at the group of ANBU and Anko with Zero he said "Hmm...who is this."
Anko said "I found this guy in the forrest of death in a clearing where several of the giant tigers were dead. He said his name is Zero and he speaks a language I heard back when I was with him. He can understand out language some. I brought him here to find out what to do with him."
Zero looked at the Sandaime and the Sandaime asked "Where do you come from and why are you here."
Zero still speaking the language Anko knew said "I am from a distant land and I am gathering info on these lands for my nephew."
Before Anko could translate the Sandaime said "I see."
Anko said "You understand him." looking a little shocked.
The Sandaime said "Yes I know the language you are thinking he is speaking but it isn't actually the language he is speaking. The last country to use the language he is speaking was destroyed years ago. Tell me, why is your nephew interested in our lands and what kind of information are you gathering."
Zero said "If I may ask, do you have a library."
The Sandaime said "Yes...why."
Zero said "Because I do not understand what you said and I would like to read your language a little to better understand what you said before I start to explain. I do not want to say one thing and find out in your language it means something else."
The Sandaime said "But that will take years to learn our language."
Zero said "No. I only need 48 hours."
The Sandaime thought a moment and said "Alright, 48 hours...but I would like to see what you look like under your mask."
Zero said "I do not trust you yet and you do not trust me. You can assign a guard to watch me but I will not remove my armor until I know if you are reploids or mavericks."
The Sandaime frowned and then looked confused and said "Mavericks...reploids...what are those."
Zero frowned and said "If you can give me 48 hours to study your library I can answer your questions. I have already stated my reasons to not answer now."
The Sandaime pursed his lips and said "Very well...Anko, ANBU, take him to the library and watch him. He said he needs 48 hours to study our language to answer my questions. If after 48 hours he refuses to answer them then I will send him to Ibiki."
Zero saw the others in the room nod and they lead him out of the room.
After a few minutes they came to the public library and went inside and Anko said "Have fun gaki."
Zero looked around and walked over and picked up a book and opened it and then after a few seconds turned the page and another few seconds turned the page and another few seconds turned another page.
Anko said "Aren't you going to read them gaki instead of just glancing at them."
Zero ignored her and kept going through the pages.
Anko said "Whatever." as she sat down.
A few minutes later Zero closed the book and picked up another and continued to do the same as before.
Inu walked over to Anko and said "What do you think."
Anko started to say something when Zero said "I think you shouldn't speak about people behind thier backs."
Everyone was wide eyed as Anko said "I thought you didn't speak our language."
Zero said "I didn't. The first book I read was a dictionary and the second book I am working on right now is a thesaurus. It has the thhes of how to say and prenounce words in your language."
Anko said "What was that word you used the thhease or whatever it was."
Zero stopped and looked at her a moment and said "I don't know how to say that word it your language yet but it means the accent of the words."
Anko said "Oh...but how did you learn our language so quick."
Zero said "I'll explain later." as he went back to reading.
Anko frowned and sat back down.
To the shock of everyone there, after 48 hours Zero was still awake and was over 3/4 of the way through every book in the library.
A beeping noise drew everyones attention and Zero said "48 hours as agreed. I will speak with the Sandaime Hokage as I have much to discuss with him."
Anko who had slept some in the library asked "How the hell are you still awake and not even need a restroom or lunch break."
Zero said "I have my ways. Shall we proceed."
When they got to the Hokage office the Sandaime said "So Zero, were you able to learn our language."
Zero said "Yes." in the same langauge as everyone else.
The Sandaime said "Good, now can you explain where you come from and why you are here."
Zero said "I can but I ask that what I have to say be only heard by you Hokage-sama. It's a very sensitive subject...like what was so special about the Shodaime and Yondaime's wives."
The Sandaime's eyes widen as did Inu while everyone else seemed confused and the Sandaime said "I'll agree but I request one guard."
Zero said "I assume you mean Inu since he reacted to what I said a moment ago."
The Sandaime frowned and nods and Zero said "Very well."
The Sandaime said "All of you are dismissed but you are forbidden to speak about anything that you saw or heard since encountering this person. Do you all understand."
Anko and the other 3 ANBU said "Hai." before he dismissed them.
After they were gone the Sandaime put up a privacy jutsu and said "Now how do you know about that."
Zero said "Tell me, what do you know about Minato Namikaze origins."
Hiruzen said "Minato was an orphan...why."
Zero was quite a moment and said "I can explain it but you won't believe me without proof...I know. Would you mind if I gave a small demonstration using one of your chairs. I think if you would allow me to demonstrate what I want then you will be able to believe the rest of what I have to say. Will you allow me to demonstrate on one of these chairs."
Hiruzen nods with a confused look on his face.
Zero said "Thank you." as he raised his arm up before his hand sunk into his arm and his arm was surrounded in a piece of metal that began to glow before a ball of energy shot out of the tube and hit the chair destroying it.
Hiruzen and Inu both were wide eyed and in a defensive stance while Zero changed his hand back to normal and said "That ball that destroyed that chair was similar to the Rasengan, was it not."
Both men blinked and Hiruzen asked "What was that."
Zero said "An energy blast."
Hiruzen said "I want you to explain why you used that now."
Zero said "In order to explain the origins of the man you know as Minato Namikaze...or as I know him as...megaman."
Hiruzen pursed his lips and said "Very well...tell us your story but know that I reserve the right to demand proof."
Zero nods and said "The world as it is now is not the way the world has always been. Before the time of the man you know as the Six Realm Sage, human beings had grown and advance to a point and time where they would replace their organs with machines that did the same things as their original organs giving them longer lives, increased strength, higher intelligence and many other advantages. They also created a race of machines called reploids who were machines that looked like humans but were designed to do certian things that humans didn't want to do like cleaning, cooking, gardening, fighting fires, and other things of that nature when they could be enjoying life. As such over time humans began to die out or became more and more machine like while reploids became more and more human like until both races could no longer tell each other apart. It was decided by the people of the world there was no longer a real human race, just the race known as reploids. Time passed and the world prospered for many years...unfortinately with all good things, eventually something happens that causes a change in the world...this change was known as the Sigma virus."
Inu said "Would you please be serious."
Zero reached his left hand up to his right elbow and grab his arm and twisted and when he did there was a pop noise and then to Hiruzen and Inu shock they saw his arm wasn't real but instead had microchips and metal in it and Zero said "I am being serious." as he reattached his arm.
Hiruzen said "Your a reploid."
Zero said "One of the last full reploids, yes. The man I call father and myself are the last 2 full reploids on our world and the last to know the history of the world. Both of us our over 3000 years old though our time is coming to an end soon...which is why my brother was sent to Konoha."
Hiruzen asked "Your brother...wait, you don't mean...as his eyes widen.
Zero reached up and took off his helmet and Inu and Hiruzen eyes widen as they saw the resemblance of Zero to Minato and Zero said "Yes, Minato Namikaze or as I know him as Megaman was my brother."
Inu said "Then your nephew is..."
Zero said "Naruto Uzumaki Namikaze."
Silence went through the room for several minutes and Hiruzen said "Why did you take Naruto."
Zero said "To protect him from the Sigma virus. The being you know as Kyuubi is in fact a maverick, a reploid who has been corrupted by the Sigma virus. When Megaman was sent here his memories of his life as a reploid was sealed away in order for him to fit in and live a normal life while also preparing to help the world for what it to come."
Hiruzen asked "What do you mean by what is to come."
Zero said "I told you how the entire world had became reploids until the Sigma virus came. I did not tell you what happened after it appeared or how life on this planet did not end by being destroyed by the sigma virus's corruption. You see, the sigma virus turns a reploid evil. It drives them to take pleasure by causing pain, suffering, and destruction...when they reach this point they became known as mavericks. Millions died by the hands of mavericks and thousands of mavericks were killed to stop the spread of the Sigma virus. Megaman and I were both 2 of the main Maverick hunters in the world who hunted down and killed the mavericks while protecting the reploids...I won't go into the details of what the world was like at that time besides saying the entire world look like a warzone."
Zero closed his eyes and said "To ensure the survival of the world the top scientist in the world got together and it was decided in order to be able to take 2 steps forward we had to take a step backwards. All the human DNA left in the world was brought together to be studied and eventually cloned...slowly over 200 years the scientist rebuilt the human bodies while also leaving the ability to return the world to it's former glory...you all take for credit what you call Chakra...Chakra is not exactly what you think it is. Chakra is in fact the power created by nannites inside your bodies. Nannites are microscopic machines that are smaller then red bloodcells. These nannites were created by the scientist in order to allow the world to head forward in the direction it had once been...however a problem arose nearly 400 years ago. The man you know as the Six Realm Sage did not help the world but put the entire world in danger...he discovered the body of the only remaining maverick which still contained the Sigma virus and he used it to create the Bijuu and passed the Sigma virus onto them. You village founder, Hashirama Senju gave 8 of the Bijuu to other nations hoping to bring peace to the world while keeping the Kyuubi here...He in fact may have caused the destruction of the world by helping to spread the Sigma virus...Right now nearly every man woman and child in the world has been infected by the Sigma virus and it is beginning to effect the people of the world. You have both seen proof of this by looking at people in your village and thinking about thier actions and how they changed over the years...even yourself Hiruzen Sarutobi...after all, you justified the death of over 200 men, women, and CHILDREN by thinking it's for the greater good...even if the parents were a threat, what threat were the children."
Inu looked confused while Hiruzen eyes widen and Zero said "Think about your own student Orochimaru how he changed over the years, how people became nothing more then test subject for him in order for him to complete his own goal."
Hiruzen frowned and said "Are you here to destroy us."
Zero said "No...as I said, my time is nearly up...the torch has been passed on to the next generation. My nephew will be coming to Konoha within a year. When he comes he will bring something that will give you and the people of the world a chance. The Kyuubi and the Sigma virus has both been removed from him and destroyed. He will either succeed and save the world and or fail and destroy the world. He is but one person. If he can gain allies and grow stronger then he will save the world. If he stands alone he will fail and the world will be destroyed. It is your choice if you wish to stand by him or against him. I ask that you both keep what you have heard a secret and think about what I have said...If you wish to help him then think about people you know who are like Orochimaru. Those who have become nothing but mavericks who only care about themselves and thier own goals and cause pain, suffering, and destruction to everyone in thier paths. Make a list between now and the time my nephew arrives. Do not judge him for his age because even though his body is young his mind is not...you are an example of what I mean Hatake Kakashi. A child prodigy. He is your last and only hope. Goodbye." as he was covered in a white light and disappeared.
Inu looked at Hiruzen who was looking down and Hiruzen said "I am beginning to question every decision I have ever made Kakashi...I look back at them and I find myself lacking."
Inu said "Hindsight is 20/20 sir...what should we do."
Hiruzen was silent a moment and said "Kakashi...I think we should do what he said...but we should also watch ourselves. Keep what you have seen and heard quite but lets hope for the best and prepare for the worst."
Inu said "Yes sir. Is that all."
Hiruzen said "At least we know Naruto safe."
Inu said "Yes. That is something to smile about."
Hiruzen feeling the smirk behind the ANBU mask said "Go get lost on the road of life Inu before I send you to catch Tora."
.5 seconds later Inu was gone in a swirl of leaves.
Hiruzen chuckled and thought "I wonder if Tora is also infected with Sigma. Might explain why she's such a demon cat."