Disclaimer; I don't own Naruto are Metroid.

Basing Samus's abilities off of Metroid the other m, and the manga version of Metroid to refer to her child hood. For Naruto it will start right after Naruto beet the shit out of Mizuki. Then will go on to Samus explaining to the Hokage her past and how it involves Naruto. After that I will return to the Naruto story line. Until after Naruto has completed his training with Killer Bee. After that Samus and Naruto will leave the paint to finish the story, with the story line of Metroid the other M. Also if you want I could also pair Naruto along with Samus the AI from Metroid the other M, also known as MB.

Authors (opinion)

Character "talking"

Character 'thinking'

Character "demon talking"

Character 'demon thinking'

Story Start

Samus Aran had just finished announcing her defeat of the Metroids. As she headed back to her spaceship. All the while thinking in her head 'It's finally time I can finally see him again.' It was time for Samus to return to the elemental nations.

Two weeks later

Mean while with are male protagonist (if you don't know who I'm talking about I'll give you a hint, he has blue eyes, whisker marks, and blonde hair.) is now panting on the forest floor, right next to a tool shed. All the while with a smile that only he can produce he yells "alright I finally got one down!"

Our favorite blond hero then hears footsteps approaching him. He then looks up to see a ninja with a scar on his noses and brown hair tied up into a spiked pony tail. The man then said in an annoyed voice "Hey Naruto". Naruto brings his hand behind his head and laughs nervously. "Oh man you already caught me. I only managed to learn one technique."

The scared teacher that we can now identify as Naruto's teacher Iruka, then thought 'he's practiced tell he was worn out?' Naruto then said in an excited voice "hey I'm going to show you a great technique, then you'll let me graduate right". Iruka then said "Naruto who told you that?" The blond then said "Mizuki-sensei told me that." The whiskered blond then turned around and continued "He told me all about this place and the scroll." If Naruto had turned around he would have noticed the horrified look on Iruka's face.

All of sudden Iruka heard a noise. Going off of his instincts he pushed Naruto aside, as he was stabbed by a mutable kunai. Right after that a voice filled the air "I'm surprised that you found out about this place." Iruka then looked up with some difficulty "So that's what's going on."

In the tree you see a silver haired chuunin with two fuuma shurikens strapped to his back. As Mizuki looked down on them he yelled out "Naruto give me the scroll!" Naruto looking back and forth at his to teachers with a scared look on his face said in a confused tone "Hey…what's going on here!"

Iruka panting pulled out a kunai from his leg and said "Naruto, don't let him get the scroll no matter what. That is a dangerous scroll that has forbidden techniques. Mizuki used you to get a hold of it!"

As soon as Iruka said that Naruto tensed up. Mizuki then looked down on them with a smug grin and said "Naruto, Iruka is afraid of you possessing that scroll." Naruto then get's a terrified look, as he hears one of the few people he thought that liked him, my not be entirely sincere. And stumbled out a "what?" While he looks at Iruka with a betrayed expression. The scared chuunin yelled "What are you saying Mizuki?" All the while looking at Mizuki with a look of pure hatred. He then turned to are whiskered hero "Don't believe anything he says Naruto."

Mizuki then started laughing "I'll tell you the truth." Iruka then screamed out at the top of his lungs with a look that is mixed of both fear, and rage "DON'T!" Mizuki then continued in almost a bored fashion "A rule that was created after the incident 12 years ago."

Naruto with a terrified expression says "a rule?" Mizuki then continued "It's a rule that only you, Naruto, cannot find out about." Are blond hero says "Only me? What's that rule?" Iruka yells out "Stop, Mizuki!" Mizuki then continues with an evil grin (Seriously is this guy taking lessons from Orochimaru.) "It's a rule not to say that Naruto is a monster fox."

Naruto eyes widened and whispered out the only word that could come at that moment "What?" The silvered haired cununin responded "In other words, you are the nine-tailed demon fox who killed Iruka's parents and destroyed our village." Iruka then screamed "Stop" for Naruto his whole world came collapsing down. It finally made sense all the glares, cruel words, and beatings. They all finally made sense now.

Mizuki then knowing that he had gotten to Naruto continued in a mocking tone "You have been deceived by this village this whole time. Didn't you find it strange why everyone hated you so much?" Naruto then started to let off enormous amounts of chakra yelling out "damn it, damn it, damn it, damn it!"

In space

Samus monitor suddenly started beeping. She smiled and whispered out "I've found you, I've finally found you Naruto-koi" Samus then hit a few buttons on her ship and changed her course.

Back in the elemental nations

Iruka looked at Naruto with a look of worry 'Naruto' he thought. Mizuki then yelled at Naruto "No one's ever going except you! Even Iruka hates you!" After that Mizuki took one of the fuuma shuriken off of his back and throw it at the distraught thirteen year old yelling "DIE NARUTO!" Naruto then fell to his knees and tried to crawl away. Iruka then yelled "Duck Naruto!" so Naruto stuck his hands over his head and closed his eyes. Right after that a heard a noise of someone getting stabbed.

Seeing that he didn't feel any pain he looked up to see Iruka with the fuuma shuriken in his back. (Seriously how did that miss his spine it was dead center in the spiral on his back.) While Naruto was staring up in shock Iruka started to cough up blood on Naruto's face. Meanwhile Mizuki who saw all this had a shocked look on his face obviously not expecting Iruka to do that.

Naruto the first to overcome the shock asked his teacher "W-why…?" Iruka then responded with a series look on his face "Because you are the same as me. After my parents died no one complimented me or recognized me. Being the bad student I was, I screwed up a lot during class… because I wanted every ones attention. I couldn't get anyone's attention when I was a good student… so I acted like an idiot. It was tough… right, Naruto? You where lonely, right?" Iruka was crying at this point as he brought up emotions that he had burred years ago. He then continued "It was tough, right? I'm sorry, Naruto. You didn't have to feel that way if I was more aware."

Mizuki who had been silent up to this point yelled out "Don't make me laugh! Iruka has hated you since you killed his parents! He just wants to get the scroll back!" Naruto not knowing who to trust any more decided to run off into the forest. As he did this Iruka yelled out his name "Naruto! Naruto!"

Mizuki then jumped out of the tree and said "Naruto's not the type to change his mind. He's going to take his revenge on this village with that scroll. You saw his eyes, didn't you? It was the eyes of a monster fox."

Iruka then ripped out the fuuma shuriken from his back and said "Naruto won't do that!" He then turned around to face Mizuki and throw the fuuma shuriken at him. Mizuki moved out of the way with his eyes closed. He then said to Iruka "As long as I kill Naruto and get that scroll, I'm okay. I'll tack care of you latter." He then jumped off to find Naruto.

In Hokage tower

Sarutobi saw the whole thing throw his crystal ball. He began to think 'this isn't good. Mizuki told him the secret. Naruto is more unstable than ever. He might release the power that has been sealed. He also has the scroll of sealing. The possibility that he will unseal himself and turn into a nine-tailed fox is possible. If that happens…"

Back in the forest

We see Iruka running throw the forest he spotted Naruto running throw the trees 'found him' he thought. Iruka the n yelled out to him "Naruto! What Mizuki said back there was a lie! Hand the scroll over to me Mizuki is after it!" As soon those words left Iruka's mouth Naruto jumped at Mizuki and punched him with everything he had.

Iruka when he hit the ground said "W-what… how, how did, how… did you know that I'm not Iruka." As Iruka showed that he was really Mizuki. Naruto sat down at the base of a tree and said "I'm Iruka" as Naruto showed that he was really Iruka.

Mizuki then stood up as he replied "I see" all the while neither of them noticed that the real Naruto was hiding behind one off the nearby trees. Mizuki then continued "what good is it to protect the one who killed your parents?" Iruka then said "I'm not going to let an idiot like you get that scroll." Mizuki then said "you're the idiot. Naruto is the same as me." Iruka with a completely straight face then said "the same as you?"

Mizuki decided to elaborate "anything is possible with that scroll. There's no way Naruto, that monster fox, won't use its powers." Iruka then said "Yea, your right." Naruto couldn't believe his ears and had a hurt and shocked look on his face and whispered "I knew it. Iruka-sensei doesn't recognize me inside." Then suddenly Iruka elaborated "If he was a monster fox. But Naruto is different. He's…he's an excellent student that I recognize. He's hardworking, earnest, clumsy, and no one recognizes him. He knows the pain of others. He's not a monster fox. He's Uzumaki Naruto of Konoha!"

Naruto was crying tears of joy after hearing those words. Mizuki on the other hand looked like he heard the stupidest thing ever. The silvered haired chuunin then stated "What an idiot. Iruka, I said I would kill you later, but I take that back. DIE NOW!" He yelled as he started twirling his last fuuma shuriken at high speeds.

As Mizuki charged at Iruka fuuma shuriken in hand Iruka thought 'This must be the end…' when suddenly out of nowhere Naruto appeared and rammed into Mizuki. Witch sent the fuuma shuriken flying off into the random forest. As Mizuki went flying courtesy of Naruto ramming him.

Naruto came to a skidding stop. Mizuki then while on his hand and knees yelled out "damn you…" Naruto then with a dead serious look on his face then said "Don't lay a finger on Iruka-sensei. I'll kill you if you do." He changed to a face that was filled with so much rage that if looks could kill Mizuki would be six feet under.

Mizuki not the least bit worried about this said "Talk while you can. I'll finish a kid like you in a flash." Naruto with his hand in a crossed shaped seal countered with Try, jerk. I'll do a thousand times more damage back to you." Mizuki pissed off at this yelled at Naruto "Why don't you see if you can, you monster fox!" Naruto then yelled at the top of his lungs "Kage Bunshin no Jutsu!"

Suddenly there was a huge explosion of smoke. Once the wind blew the smock away, to Iruka's and Mizuki's they were suddenly surrounded by hundreds of Naruto's. Iruka thought 'Naruto you used kage bunshin no jutsu? It's a high class technique where you create a real body.' Mizuki was absolutely in shock to see the dead last use such a high class jutsu stammered out a "W-what…?"

The Naruto clones started to antagonize Mizuki and yelled out "What's the matter? Come get me. Come on." Then certain clones started to talk in tangent "If you're not coming… where coming!" Mizuki knowing that he's lost yells as loudly as he can "YAAAAA!"

(The beat down that happens in this scene is too violent to describe.)

You see a Mizuki that has been beaten into a bloody pulp lying on his back at the feet of Konoha's most hyperactive knuckle headed soon to be ninja. Naruto laughed and scratched the back of his head and said to Iruka "Maybe I hurt him too much. Iruka-sensei, are you ok?" Iruka responded "yeah…" On the inside however he was thinking 'what a guy… he might really surpass the previous Hokages.'

Smiling with a bit of effort Iruka said "Naruto, come here for a second. I want to give you something." Naruto obediently walked over to his teacher he then closed his eyes. He then heard some metal moving around so he asked Iruka "Sensei, are you done yet? Iruka replied by saying All right, open your eyes."

When Naruto opened his eyes he saw a smiling Iruka standing before him without his headband and holding his goggles. Iruka then said "congratulations. You graduate" Naruto just stared at Iruka in shock. Iruka then sighed and said "All right, let's celebrate. I'll treat you to some ramen!"

Naruto responded by doing a flying hug at Iruka yelling "Iruka-sensei!" Iruka who fell over and had his back hit a tree right where he had been stabbed said "Ouch! That hurts!" Naruto and Iruka got up to head back to the village. They saw a huge orange vestal flying throw the forest and landing a little bit away from them.

Naruto said "Iruka-sensei I'm going to go check it out." He ran off before Iruka had a chance to tell him not to.

At the ship

Samus parked her ship in a small clearing. After she left the ship in her zero suit. Before she left she used the stealth function on her ship so that no one would see it. Samus then started to walk toured the village. When she heard someone yell "halt right there!" She scoffed and turned around to look at who it was only to freeze once she saw him.

Naruto had just arrived at where he thought the ship might have landed; where he saw a blond female in a very tight blue outfit. Naruto did the thing any ninja would do when they see a stranger and yelled "halt right there!" Our favorite male blond saw her turn around and look at him then freeze so Naruto said "are you alright lady."

All of sodden before Naruto could move the girl was next to him hugging him into her very impressive bust. This was the sight that Umino Iruka was greeted by before he properly passed out from a large nose bleed. This however went unnoticed by the two blonds.

Naruto was kind of confused as to why this girl; no not girl women was hugging him. He would be lying if he said it didn't feel nice however he was unused to people suddenly hugging him. Naruto forced himself to look up to his face and was shocked to see her crying.

Naruto finally worked up the courage to ask "um who are you?" He was surprised when she flinched back as if he had slapped her. Before she calmed down smiled and said "That's right you wouldn't remember me. My name is Samus Aran, and you are Naruto Uzumaki someone who is very dear to me." Naruto looked confused for a second until he turned around and saw his teacher on the ground with blood coming out of his nose. Naruto sweet dropped and ran to his teacher.

While he was attempting to shake his teacher to wake him up. Samus smiled 'even if Naruto didn't remember me he was still the man that I fell in love with. It still hurt that he couldn't remember me, but I couldn't blame him especially after that had happened".

Samus was snapped out of her thoughts when Iruka woke up. She walked over to them and said "please take me to your leader I have things that I must talk to him about." Naruto then enthusiastically yelled "You want to see the old man Hokage." When Samus nodded Naruto grabbed her hand and ran off.

Pore Iruka forgotten sighed and decided to head to the hospital 'after all that women's chakra reserves where so low that even a sensing type like Iruka couldn't detect any chakra. How dangers could she be?' Iruka never knew how wrong he was.

In Hokage tower

Naruto had just left the office, and left Samus with the Hokage to talk. Samus then started the conversation "I assume you want to know what I want with Naruto?" Sarutobi nodded and gestured for her to continue. Samus then stated "While I hope you're in the mood for a story because, this goes back to when I was tree and I lost everything. Only to gain what is most important to me."

Story end

Ok my first try tell me what you think and how to improve. Hope you liked it.