A/N: Hey I bet you didn't see this coming! :D Yeah NarutoxPrototype! So yeah, always had some ideas for Prototype; strengthened forms for his weapons, augmentations to the armor form for each change, etc. Hope you enjoy it.

UPDATE: Fixed a major flaw in Alex's description from Prototype 1. How come no one noticed that? ._. We're in chapter 5, people, and it took TheArchive the point it out. Rather politely I might add. (See, GodShadowEX; THATS how you point out flaws! :D Suck it!) Anyway, thank you again, sir, for pointing this out. My memories are hazy of the game so I ended up interpreting Alex as a good guy. Shame on me.

Disclaimer: I do not own Naruto or Prototype

"Hey"- Human Speech

'Hey'- Human thought

"Hey"- Jutsu/Demon speech/Blacklight Technique

'Hey'- Demon Thought

"Yeah! I did it! You'd think taking something like this for a test, they'd make it harder." Naruto commented as he jumped through the forest, the Forbidden Scroll of Seals strapped to his back as he headed to the meeting place. He merely used the Oiroke no Jutsu to knock out Jii-san; the pervert! He stole, what he thought, was the fake scroll for his test Mizuki-sensei told him about after he failed his Genin exam.

He landed down, preparing for the second phase of his 'secret' test: learn a technique from the scroll. He set the scroll down, unrolling it, and read the first technique he saw. 'Hmm Kage Bunshin? Aw man, not another Bunshin; I suck at those. Eh, maybe this one will be different.' He thought, reading the notation for the technique and started training on the Kage Bunshin.

An hour later, he stood in the clearing, panting, but happy, as he successfully did the Kage Bunshin no Jutsu, a technique that created solid clones of himself instead of the illusionary clones of the Academy Bunshin. He returned to the scroll, looking over some more techniques; hey, maybe the more he learned, he might get extra credit and they'd have no choice but to make him Hokage!

He noticed a seal at the bottom of the scroll, as well as a note to the side of it.


This seal holds the power of a deadly Kekkei Genkai from a pair of men who could surely surpass all Kage's, past, present, or future. Their names were Alex Mercer and James Heller, and they held the power of Blacklight.

If you believe you can carry the burden of this power, just use your blood and chakra on this seal, and inject the virus in your system. If you survive, it is a sign you will control this awesome power... or Kami is toying with your emotions and has decided to make you wait for your painful death.

Who's to say?'

As he read this, the color from his face faded, especially at the mention of the 'if you survive this' part; he didn't know if he could do this. Then he thought it over, he was Uzumaki Naruto, dammit! The kid who would be Hokage! He can do this!

'I'm pumped! I'm pumped! I'm pumped! He chanted in his head. With renewed determination, he slapped his hand on the seal, sloppily flaring his chakra into it, only for nothing to happen. He sweat dropped at how Kami seemed to be fucking with him but then remembered the note mentioned blood. So, biting his thumb to draw blood, he repeated the process, to the results he expected: a puff of smoke. Waving his arm around and coughing a bit, he cleared the smoke away, showing... a syringe. He felt his eye twitch at the sight of the medical device; he always had a fear of needles. Who wouldn't?! Their sharp pain as they entered your skin, the feeling of cold steel inside you, the fact they are actively trying to draw blood unnerving him to no end. Steeling his resolve, he retrieved the needle and outstretched his arm, preparing for the searing pain that is the needle. He stabbed himself and squeezed the end of it, gritting his teeth at the cold feeling of the needle in his arm and the initial pain of its entrance. Then, his world became red and black, like a writhing mass. His body was drowned in pain as his body writhed in it, his very DNA screaming in pain at him.

The process lasted the remaining amount of time he had to wait for Mizuki, an hour. But the pain slowed that time, making it feel as if it were days. About five minutes before Mizuki was to arrive, everything stopped. His body still, the pain gone, his vision, returned, but blurry. He steadied himself to his hands and knees, panting heavily, feeling so exhausted, a feeling incredibly alien to him; he had never become exhausted a day in his life. He heard a rustle of leaves behind him, but made no effort to acknowledge it, only concentrating on the new feeling that he felt after he got passed the exhaustion. He couldn't truly describe the feeling it gave him, it made him feel heavy, and cold.

"Naruto! What do you think you're doing?!" A familiar voice yelled at him, making him stiffen and pausing his heavy panting. Slowly turning his head, he looked at the man talking to him with one eye, the other shadow by his hair that seemed to have grown, looking at his sensei, Umino Iruka.

"H-hi, Iruka-sensei." Naruto said in a strained, but slightly deeper, voice.

Iruka's eyes widened at his student; he had changed quite a bit. His hair was slightly longer, now falling down his neck instead of the mop on top of his head. From his angle in the trees, he could tell Naruto had spontaneously grown a toned build, like a veteran Chuunin, maybe a rookie Jounin. But his eyes, or rather eye, surprised him the most; from the one he could see, what was once a cerulean orb among his white sclera, now there was a faintly glowing orange ring amidst a sea of black, giving him an ominous look under the shadows of his hair. "Naruto, what happened to you?" Iruka asked.

Naruto merely shrugged, an action that strained his sore muscles. He struggled against the pain to turn around and just let himself fall on his back, showing the hidden eye was his normal cerulean, slightly relieving Iruka that something had happened to Naruto that could effect his... condition. "I dunno, Iruka-sensei. But I learned the technique, so I pass the secret test, right?" He asked tiredly, confusing Iruka further.

"Secret test? What are you talking about?" Iruka asked.

Naruto frowned, confused. "Mizuki-sensei told me about a secret test I can do to become a Genin, since the public test was my last chance. Don't you know about it, too?" Naruto asked, only adding on to the mountain that was Iruka's confusion.

"Naruto!" A voice called, a figure appearing on a branch overlooking the mentioned blonde. Both people arleady on the forest floor turned to face the voice, seeing Mizuki. 'Dammit! Iruka's here! I didn't expect him to find Naruto before me! Guess I have to go about this as tactfully as I can.' He cursed in his head. "Naruto, give me the scroll and you pass your test!" Mizuki demanded, his hand outstretched.

By this time, Naruto's insane stamina had recovered his energy and he was now leaning against a tree, on both feet, holding the Forbidden Scroll of Seals. "What's going on, Mizuki-sensei? Why doesn't Iruka-sensei know about the test?" Naruto asked shakily, both Chuunin mentioned noticing he had grown a few inches taller and his horrid orange jumpsuit was torn at the top, showing, surprisingly, a muscled torso, something that confused both men; the boy didn't eat healthy, only having ramen for breakfast, lunch, and dinner, and no amount of exercise he might have down could have given him the physique in the time between his stealing the scroll and now. They had barely even noticed a web of thick veins sprouting from his right arm, pulsing red now and then.

Deciding for himself this new change was the last straw, he decided on a different tactic. "Naruto, would you like to know why everyone in the village hates you?" Mizuki asked, an evil grin slowly forming on his face.

Iruka's eyes widened as he listened to Mizuki. "No, Mizuki, don't! It's forbidden!" he yelled.

Ignoring him, Mizuki continued. "I'll tell you the reason. 12 years ago, when the Kyuubi no Kitsune attacked Konoha, the Yondaime fell the great beast." He started.

"He killed it, right?" Naruto asked, slightly shaken at the situation.

"No, even the great Yondaime could not destroy a demon, let alone the strongest. So he sealed it away, in a newborn baby. The day this happened was the day that baby was born, the child the only one born on that day: October 10th." He continued, relishing at Naruto's widened eyes at what he was insinutating.

"MIZUKI!" Iruka yelled again, trying desperately to get him to stop.

"He sealed the child inside you! You hold the Kyuubi no Kitsune inside you, the demon that killed everyone we all loved, including Iruka's parents! You are the Kyuubi no Kitsune!" Mizuki finished rather insanely, lifting a fuuma shuriken from his back.

"You're wrong!" a voice yelled, as two figures jumped from the canopy to stand between Naruto and Mizuki. The first man, the taller of the two, was a dark skinned bald man. He might be from Kumogakure, Iruka mused. He wore a dark grey trench jacket over a black sweatshirt hoodie with red interior, an odd set of dark blue pants (only weird to the Naruto-verse, jeans), and black combat boots. He had a scar on his left eyebrow and he was currently scowling.

The second shorter of the pair was a lighter skinned man, around Mizuki's tone. He wore a black leather jacket with two white bands on the right sleeve, with some odd red tribal wing design on the back, over a brown hoodie, which he wore covering his head, and a white dress shirt with the collar folded out. He wore the same pants as the taller man, but a lighter shade, and shorter brown boots. He seemed to have a blank look on his face as he glared at the Chuunin before him.

"Who the hell are you two?!" Mizuki yelled at the strangers.

"No one you need to care about! Yo' ass is going down!" the darker man replied rather crudely, his arms erupting in clouds of writhing black and red tendrils, revealing pulsating red and black arms with spikes sweeping up, looking like they were made of solid steel, all leading into his new hands; four huge claws, slightly serrated nearing the 'knuckles,' also shining as if they were made of some kinda of steel.

"I assume you want to handle him, Heller?" The shorter man asked sarcastically.

"You know it, Mercer!" The darker man replied, lunging at the shocked Chuunin with his new claws.

Mizuki just barely managed to knock himself out of his stupor and dodged the mutated man, but losing his left arm in the process. He yelled at the pain and clamped his hand over the stump to stop the bleeding. "Why do you attack me?! I have no idea who you are so I know I didn't do anything to you! Attack the boy, he is the Kyuubi!" Mizuki defended himself, only to receive the loss of his remaining arm via a blade extended on a rope-like extension of flesh, covered in spikes of the same steel-like material, vaguely reminding him of a spine, as long rounding tubes of more spikes traveled up the mans newly change right arm, the left still clawed. He yelled at the horrible pain as he fell to his knees, the blooding drooling from his wounds.

He looked up at the shadow looming over him, seeing the same dark man that was destroying him, silently begging for release. The man complied, his arms returning to normal as he grabbed Mizuki by his sides, lifting him into the air and performing a German suplex, shattering Mizuki's skull with his strength-augmentation, and finishing it with shoving his fist through the stomach, his arm erupting in the same mass from before that changed it to the claws, only the seized the body their host limb was piercing, converting it into a large, fucked-up-Mizuki shaped cloud of the mass as it was absorbed into the mans body.

He gritted his teeth and held his hand to his head as the memories flooded his mind. Instead of going through the majority of them, he merely skimmed through the whole point of them. "He was planning on killing you and bringing the scroll to Orochimaru." He said to Naruto gruffly, confusing the boy who was slightly green in the face at what he just witnessed.

He stood up and puke into a nearby bush, having witness his first kill, a rather brutal one at that. Panting, he slowly stood up straight, keeping a hand on the scroll and tensing his muscles for a escape in case these men were going to kill him next. "Wh-who are you?" He asked shakily.

Instead of the large man who slaughtered Mizuki, the shorter man answered. "We are here because you injected yourself with the Blacklight; you did this, correct?" He asked, receiving a shaking nod from Naruto. "Then if you read the warning, you know our names already. I am Alex Mercer, and my... associate is James Heller." He answered, his 'partner' walking over to stand next to him again.

"S-so, I have your Kekkei Genkai? How is that possible? I know Kekkei Genkai can only be passed through blood relations, and I don't think I'm related to either of you." Naruto asked.

"We merely called it that so as not to arouse suspicion; it is, for all intents and purposes, not a Kekkei Genkai. It is a virus, plain and simple. You infected yourself, survived, and so you now have the Blacklight virus like us." Alex reassured him, receiving a nod of understanding.

"So, now that you have Blacklight, we gotta train yo' ass in it." James added, eliciting a sigh from Alex.

"Smooth, Heller, smooth." Alex muttered under his breath.

"Um, excuse me, but could someone EXPLAIN WHAT THE HELL IS GOING ON?!" Iruka interjected, using his famed Big Head no jutsu for emphasis, as he was just plain confused now.

"Bitch, shut the hell up." Heller retorted, causing Iruka to shrink back. "We're gettin' to that!" He added.

Alex slowly walked to Iruka and tapped his finger on his forehead, flooding his mind with the explanation, including the fact they are now Naruto's official sensei's, including whoever will be his shinobi sensei, so as to teach him the ways of Blacklight while the sensei, hopefully, teaches him the shinobi arts such as ninjutsu and taijutsu.

Iruka almost collapsed as all that was explained in his mind within a second. "S-so the changes to his body?" he asked.

"The virus modifying his body for maximum potential, as well as fixing any health problems such as malnutrition from the villagers' actions; the narrow minded fools." Alex commented, reassuring Iruka at his question and that they were not secretly against Naruto, for that had happened too many times to the boy for him not to expect it.

"Okay, whoa, whoa, and just whoa. This is a lot to take in. I just found out I hold the Kyuubi no Kitsune in me, and now you two, who are supposed to be either dead or really far from here, are going to help me on a new Kekkei Genkai I just injected myself with like a crack addict?" Naruto asked rather flatly, receiving nods from James and Alex. "Oh, okay then." He replied, then fainted, eliciting sweat drops from Alex and Iruka, and a chuckle from James.

(One hour later, in Hokage Tower)

Alex, James, and Iruka had traveled to the Hokage Tower to return the Forbidden Scroll of Seals to Hiruzen, and to explain what happened in the forest, Naruto still unconscious over Heller's shoulder.

Ignoring the protests of the Hokage's secretary, and aiming a killer intent-laden scowl at the woman for her heated glare at Naruto from James, they walked into his office, the dark man kicking the door open rather rudely, surprising the man who was reading a small orange book and giggling perversly with a blush.

"Aah, what, who?!" he yelled, sounding like some drunk who was just woken up from their alcohol-coma. "Oh, Iruka-kun, you shouldn't scare me like that. Excuse me who are you two and why are you carrying one of our villagers like he's a sack of potatoes?" Hiruzen asked, glaring at James for the previously stated action.

"Hokage-sama, something happened when Naruto stole the Forbidden Scroll." Iruka then began the explanation after returning said scroll to the Hokage.

When he was done, Hiruzen was silent, smoking on his pipe in contemplation. "So who are you two? Your lives, I mean." He directed his question to Alex and James.

Alex then began his tale of his life as a scientist working for a company called Gentek, creating a virus called Blacklight that he made from a strain given to the scientists from the mysterious woman in hope, Idaho, Elizabeth Greene. He then left the company, intending on using the virus for his own personal means, only to be gunned down at Penn Station and the virus to consume his remains and recreate his body as a host for the virus. He explained he, in fact, was no the Dr. Alex Mercer that created the disease; he was the disease. He then weaved a tale of his journey through his hometown of Manhattan, looking for answers, partially explaining his powers through the acts of consuming his victims, receiving their memories.

After Alex, James Heller spoke his tale of his life as a military soldier, seeking revenge against Alex when he released a second wave of Blacklight, supposedly killing his wife and daughter, and his adventures of Mercer infecting him and his journey for revenge, finding the help of Mercer's sister and, with her, his daughter. He then finished with the conclusion that he consumed Alex, confusing everyone since Mercer was cearly before them. He then explained how, after being consumed, Alex became a second consciousness in his mind and, using the excess biomass of his victims, created a body for Alex as a sort of partner, as his 'immortal' life of being infected would surely have driven him into madness were he alone.

A silence fell over the office as everyone attempted to swallow this information, only interrupted by Naruto's mutterings about ramen. James Heller pulled him off his shoulder and proceeded to slap the shit out of his face repeatedly until he woke up. He had to keep up the slapping for about 10 seconds until Naruto awoke as if someone shook him lightly.

"H-huh?" He muttered sleepily.

"Wake up bitch." Heller answered, emphasizing each word with another slap to the face, fully awakening Naruto with the pain.

"Ow! Ow! Ow! I'm awake!" He yelled, blocking Heller's hand that insisted on 'making sure' he was awake.

"Hello, Naruto-kun." Sarutobi greeted.

"Oh hi, Jii-san." Naruto replied, somehow appearing in front of his desk, out of James' grasp. "What'd I miss?" he asked.

"Quite a lot, Naruto-kun. But long story short, these men are going to be your co-sensei's alongside your shinobi sensei, so as to teach you the techniques of this Blacklight." Hiruzen answered.

"Okay. Can we talk about this tomorrow? I'm tired from finding out a lot of stuff today." Naruto asked, rubbing his eyes and yawning, somehow still tired even though he was supposed to have insane amounts of stamina, something from the Kyuubi, he mused.

"Of course. Tomorrow your teams will be chosen and you will meet with your sensei's. After your team does, please come back here so we may clear some things up, especially about Kyuubi and how it is affected by all this." Hiruzen replied.

Naruto merely nodded, only half-hearing him, and went home, dropping dead onto his bed. About 20 seconds into his sleep, he realized what Sarutobi said. "WHAT?!" He yelled.

Naruto's life just got a lot more complicated.

End Ch. 1

So, what'd you think? Find how he got the powers believable? How Alex is still there, kind of? Tell me what you think.

Ja ne!