A/N: And here's chapter 6. I'm glad that so many people were waiting for my last update, even if I'm sorry it took so long. Still, almost everyone liked it, and that makes me feel all warm and fuzzy inside. Looks like I won't have to torture a small furry animal to make me feel better about myself! (If you can't tell that I'm joking about that last sentence, I'm not the one with issues despite what my therapist says.)

I also learned something about myself! Apparently, I'm not the type of author that can write chapters ahead of time. When I went to release this chapter a few weeks ago, I took another look at it and said, "This is crap." And then I redid it. Twice. So yeah, I'm redoing the next chapter to compensate for the changes. And sorry for the delay on this one while I'm at it.

I'll take some time to address some of the concerns I read in the reviews. Yes, Naruto at this point in time could basically curb stomp Mercer and the entire infection, preventing any more deaths among the innocent. The reason why he's not doing that is two-fold.

First, please remember that this is a grey and smarter Naruto. Yes, he realizes that he could save many people now by doing that, but he also realizes that there's nothing stopping this from happening again. He wants to fully end this by wiping out everyone who was involved with the virus. What he's doing is taking the time to make sure that he finds them all so that no one can hide until everything blows over and start this again. He's taking the "sacrifice a hundred to save a thousand" approach this time to end it for good. He will end plots as he finds them, but for the most part he's planning on getting everyone in one fell-swoop.

Second, because I say so. I want this arc to happen, so it will, and if he just steps on Mercer then it will mess up my plans for the future. Besides, I need a specific event to occur, and if this outbreak doesn't happen then the event won't go the way I want it to.

The other thing I want to address is the fact that by Consuming Greene, Naruto should have gotten the Hive Mind ability and the ability to control mindless infected. I won't fully explain it here, it'll be revealed later in the story, but I'll just say that he got something else instead.

Finally, because some people have asked, Naruto is 10 years old at this point in time. Yeah, he's still a kid, yet more badass than anyone else besides Chuck Norris due to his life growing up and all the things he had to do in the first outbreak.

I don't own Naruto or Prototype. I wish I did. Then, you would all call me Fenerath-sama and worship the ground at my feet. BWAHAHAHA!

"Speech"

'Thoughts'

"Demon/Summon Speech"

'Demon/Summon Thoughts'

Jutsu/Skills

Chapter 6: Experiment

-The Next Day-

Naruto stretched as he worked out the kinks from his body. He had spent the last few days after meeting Heller searching for a clue as to what Mercer and Blackwatch were up to. While he hadn't managed to get a line on Mercer yet, he did find the main Blackwatch base and had camped out in any nearby nook and cranny that he could find while using his enhanced hearing to listen in on as many conversations as he could. He had even used some clones to do the same from different vantage points to make sure he got as much information as possible.

He had considered infiltrating the base directly, but since they might have had hidden viral detectors inside and around the base, he decided that it was best to not risk alerting them to his presence. If they became suspicious in any way, that might have caused them to become more guarded and keep him from learning as much as he could otherwise. Well, unless he consumed them all, but that would require risking them getting spooked and he didn't want that just yet.

Besides, this tactic paid off. He overheard talk about the disruptions that were caused by Heller, and based off of the reports he seemed to be getting stronger and evolving already. Not only that, but he also overheard reports about some testing that was going on for something called 'Orion'. This seemed to be crucial to Blackwatch for some reason, and it seemed to be related to the virus. This might have been the root cause behind their activities during the quarantine.

During his time in the city, Naruto had noticed that despite all of the protections and barriers that were put into place, not much was actually being done to destroy the virus. Blackwatch seemed to be content with containing it, which increased Naruto's suspicion of them. Based off of what he had heard while camped out, it seemed that they had no plans to save NYZ. Instead, they were planning to use the infection as a giant lab. They planned to use the quarantine and the panic and confusion from the outbreak to perform all sorts of unethical and human experiments. While they did have a possible cure that they were planning to test, it was only to make sure that they had a means to control their 'weapons', and make sure that their enemies could not use them against them.

After all of the tests had been performed, they were planning to then report that all of the contingencies had failed and that the city had been overrun by the infected. Finally, to cover their tracks, they planned to then set off a nuke in the city to wipe out all traces of their work, cleaning up after themselves.

It sickened Naruto to think that people could be so uncaring of human life. Sure, he killed when he had to, and he even killed innocents to save his own life by consuming them. However, to plan the murder of millions, just for their own benefit… how could people like that exist, yet he be called a monster for something that he had no control over. Fuck, not only didn't he have control over any part of what he was, but both him being a jinchuriki and infected where things that were done TO him by others.

Yet these people, who maim, murder, torture, experiment on, and more just because they have the power to; they get to go to their homes, have families, and get called heroes. What the hell was up with that?

Shaking himself from those thoughts, Naruto decided that he had to act. He had heard about one of the head scientists, a man named Koenig, and decided that he would have at least some of the information he needed to make sure that he could get everyone involved. So he had then waited until he discovered the location where Koenig was working from, as well as a brief description of the layout of the building.

As he started making his way to the lab where Koenig was working out of, Naruto got an odd feeling from one of the soldiers that were posted at the base. Pausing for a bit, he kept out of sight while he studied the man for a bit. He saw nothing that was unusual about the man except that he was of a higher rank than the others around him, but that wouldn't have caught his attention.

Focusing completely on the man, Naruto quickly determined what the feeling was. The soldier was infected, but unlike the majority of those infected he had kept his mind and appearance. He didn't feel like himself or Heller so he didn't seem to have the full Blacklight virus, but he was definitely not human any more. Did Blackwatch manage to weaponize the virus at least partially, or was something else going on?

With this in mind, Naruto watched the soldier and waited for him to be alone. This was a new piece of the puzzle that had to be solved before he could end everything once and for all. After an hour of observation, the man left the base and started making his way through the city. Naruto watched carefully as the soldier took a shortcut through an alley between two buildings. Taking advantage of this, he decided to not risk anything and just Consume him.

Decision made, he shifted his arm into his Blade and dropped down just behind the man, slicing the man in two from his head to his groin and burying the blade in the cement below. Quickly shifting both of his arms into his Claws, he then thrust both of them into the brain matter of each still upright half and began to Consume him. The attack had occurred so suddenly and without warning that the man had not even begun to prepare himself so was taken without resistance.

A slight headache developed as Naruto began to absorb the memories of the man he had just absorbed. It was a testament to how he had adapted to his training with Kage Bushin and how used to Consuming he was that a lifetime's worth of memories only caused his head to pound lightly and only for a few moments instead of putting him through agonizing pain or exhaustion. He quickly sorted through the newly acquired memories for relevant information as to who he was, how he became what he was, and what his plans had been.

What he found alarmed him. Apparently Blackwatch had developed a cure for the virus called Whitelight. Now, this in itself wasn't a bad thing… well, for all of the normal infected anyways. For those with the Blacklight strand it would be deadly. What truly alarmed him however was that Alex Mercer had been busy behind the scenes and had subverted the project.

Mercer had infiltrated Blackwatch, infecting key personnel in both Gentek and Blackwatch with a weaker version of the Blacklight virus that only gave the infected some of the abilities of the virus. These 'Evolved', as they called themselves, had infiltrated the Whitelight project and changed it so that instead of spreading a cure, they would spread the virus instead.

Also of alarm was the description of the Orion project, and how close they were to completion. Super-soldiers created from a variant of the virus, they had increased healing and durability, as well as surgical enhancements. There was a plan in place to lure either Heller or himself into a trap to test the abilities of the soldiers.

And speaking of Heller, apparently Mercer had caught wind him and Naruto joining forces and had begun to take steps to neutralize the threat. Naruto knew that he had to warn Heller quickly, the plan of attack was going to be swift and both would need to hurry to be able to stop them.

With those thoughts swirling through his head, Naruto quickly tried to reach Heller to warn him about Mercer's plans, but either he was busy, somewhere a signal couldn't reach, or was just plain ignoring him because Heller wasn't picking up. Cursing softly, Naruto decided to track him down quickly so that he could pass the warning along quickly.

That decided, he quickly sent out a Hunter Pulse to locate Heller and then followed the echo from where it originated. After traveling for a while, he came across a building that he seemed to recognize. After thinking about it for a few moments, Naruto realized that this building was the same one that Koenig's lab was located. Seeing the irony at how both he and Heller had both decided separately to go after the same person, he then made his way inside the building, Shifting into a mouse and sneaking past the security that was much lighter than the headquarters.

-Inside the Building-

"… developing a program called Orion. They're growing… how can I describe them… they're super-soldiers. And they're going to be sent after you, Sergeant, though you might be able to stop them, if you act immediately." Stated an old man with white hair and a full beard.

The speaker was an elderly man named Dr. Koenig, who even though was in his later years in life still had the energy of his earlier years to keep him going. He was wearing a white doctor's coat over a plain suite with a red and black striped tie. The old man had been filling Heller in on the details of Project Orion in an attempt to convince him to go to try to end the project. He had apparently become guilt ridden over time due to the experiments that Gentek had performed during his years with the company and was trying to redeem himself.

"So, what, am I supposed to just trust you?" replied Heller. As he said this, he looked around the office. It was a simple one, especially considering its occupant was one of the leading scientists, and didn't have much of note. One of the only mentionable things that indicated that the office wasn't for some mid-level clerk was that one of the walls had been replaced with glass, allowing Koenig to see into the next room. The other room had been transformed into a lab of sorts, a bloody table with restraints indicating what type of lab and experiments had been performed there. It allowed Koenig to oversee an experiment while still keeping up with his paperwork.

The more Heller saw of the place, the more uneasy he felt about Koenig, but if the information he gave is true, then he could be useful.

"Let me help you. Please. The guilt will destroy me otherwise." Begged the elder man.

Heller turned to face him. "If you're telling the truth, we'll talk more." He stated, poking a finger threateningly in his direction. Koenig had little doubt of what Heller would do otherwise.

"Please, please, time is of the essence. The head researcher's na-"

Suddenly, the tip of a Blade erupted from Koenig's head from behind. Heller stepped back in shock as incoherent gurgling sounds escaped from the former scientist's mouth, his death rattle and wide open eyes making it seem as if he was trying to pass on one last message.

"You know, for a soldier who was already betrayed and turned into a lab rat, you're far too trusting." A familiar voice sounded from behind the corpse. As these words rang out, red and black tendrils shot out and surrounded the corpse, breaking it down and Consuming it to reveal the speaker to Heller.

"Is that so? Maelstrom…" Heller glared at the boy, who still had his Blade extended where it had pierced Koenig's skull. Heller quickly shifted his arms into a form more suitable for what he felt was an upcoming battle. Naruto, on the other hand, rolled his eyes and shifted his Blade back into his normal arm.

"I was talking about Koenig." He replied. This caused Heller to blink confusedly, so Naruto decided to elaborate. "OK, quick overview since we don't have much time. Koenig was planning to send you to Project Orion, it's a trap. He and others are double agents working for Mercer. Mercer infected them with a weaker version of the Blacklight virus we have and made them his pawns. They call themselves 'Evolved'. There's something big going down soon that we'll have to stop, but that can wait for something more urgent. What you need to know now is that Mercer has caught onto the fact that I'm in the city and that we're working together, so he decided to take steps to remove you. There's an attack going on soon against someone named Guerra. Apparently he's important to you and has been helping you, so Mercer wants him gone."

Heller blinked at the information, but when Naruto mentioned Guerra, he snapped. "What?!" he roared out.

Naruto nodded in response. "We don't have much time. Either way, the trap at Project Orion needs to be sprung so that we can cripple that operation and reduce their resources. I'll take care of that, while you save your friend. I'll call you tomorrow morning to bring you fully up to speed and we can decide where to go from there."

Heller just nodded in response with narrowed eyes, apparently still wary of the blonde boy, and then dashed off to save Guerra. Naruto just shook his head and watched him go. As for himself, he had a trap to spring but first he had some preparations to make.

-Project Orion-

"Are you sure Heller's coming?" asked one of the guards who were standing around. They had gotten the call an hour ago that Heller would be making his way over to the base, but so far he had been a no show.

"Yes, we're sure." replied his partner. "Koenig himself called as Heller was starting to break into the lab. It probably just took him longer than expected to convince Heller to come here."

The other guard just sighed. The alert had been passed for everyone to prepare for Heller's arrival and engage all security procedures. The first part of the procedure involved pitting Heller against one of the Orion soldiers as a test to see how they compare. Afterwards, if Heller won, they were to use all means necessary to put him down. Despite all of this however, there was nothing going on.

Maybe Heller got scared off?

As the guard was thinking this, he noticed that a slight drizzle had started to fall. He looked up, but saw that while the sky was cloudy, they weren't quite rain clouds just yet. Not only that, but there was a break in the clouds over the base at that moment.

"… the hell?"

Looking around, he saw that the rain was only falling over the base, everywhere else was dry. Also, a faint but somewhat familiar odor was beginning to tickle the back of his nose. It was some type of fume that he felt that he should recognize, but felt so out of place that for the life of him he couldn't figure out why.

Reaching out a hand, the man cupped it, catching the drizzle and letting it pool in his palm. Taking a closer look, he saw that the liquid had a light sheen to it. Rubbing his fingers together caused him to feel how they had become slick and slippery, the liquid forming a coating due to its viscosity. Suddenly realizing why the scent felt so familiar, he felt his hackles rise in alarm as his eyes slowly widened.

"Shit." He whispered. Looking up at the other guards, he quickly began shouting. "Everyone get out! This is-"

The soldier never completed his sentence, as at that moment he, along with the entire base and everyone in it, was consumed in a massive conflagration of flames. Dozens of people who were nearby shouted in shock as they stumbled when the buildings and structures that comprised the base were engulfed in a raging inferno that was just shy of an explosion.

A few blocks away, Naruto looked on as the facility burned to the ground, all of its data destroyed along with it. He considered the damage that the attack had caused.

Gama Sekiyu Enmu (Toad Oil Haze), a jutsu taken from Minato's library that he obtained from his summons, and one of their few assassination type jutsus. Apparently it's supposed to spread toad oil in a superfine mist within a certain area, without informing the target that anything was wrong. Then the user ignites the haze, killing the target in a fiery explosion.

Naruto however did not have quite the chakra control or practice with the jutsu to produce the haze, instead creating a drizzle. While still causing a massive inferno, the larger particle size of the droplets, not to mention that they couldn't just hang in the air, reduced the impact of the blast.

That's not to mention that the jutsu in this form didn't have its uses or was a failure. When used in this way it caused the oil to pool, providing more fuel. In the end, the fire burns hotter and longer, destroying far more of the target. Still, that kind of differentiation should have been done on purpose, not from a lack of control.

For a first time use however… it wasn't bad. Considering that he used a dozen concealed clones to make sure that the entire facility was covered in the mist, the jutsu ended up working well and did exactly what he wanted it to. Not to mention that the guards at the "Proving Grounds", as Blackwatch called it, had no idea who destroyed the base so they probably still thought that Heller was on his way there.

Pleased with the results of his test, Naruto headed off to spring the second part of the trap meant for Heller.

-The Proving Grounds-

As soon as Naruto arrived, he noticed that the area was swarming with soldiers. He stood atop a curved wall, out of sight from everyone, and noticed that the area appeared to be a stadium of some sort that had been converted for Blackwatch's use. There were walls marking out a circular area, and the ground within that area was divided by a multitude of bio-locked steel crates. It seemed to be that this is where they kept all of their live test subjects when they weren't using them.

Naruto considered how to proceed. At first he thought about unleashing another round of Gama Sekiyu Enmu on the area, but he noticed that there seemed to be some guards with dogs sniffing around. He figured that they had realized what happened at the base and decided to setup precautions this time around. This time, if he were to try it again, they would quickly be alerted and start evacuating before he got a chance to fill the area with mist.

So while thinking about the next step, Naruto sat down on the wall to consider his options. He could just flood the area with clones, but he didn't want to neither show off that ability just yet nor wait for the cleanup. Plus he still wanted to try out some of his other abilities to get some practice in using them in live situations. Sighing, he leaned back and looked up, seeing the clouds which had darkened considerably since he had destroyed the base.

Suddenly, an idea came to his head and Naruto grinned evilly. Minato had theorized a jutsu in his scrolls based off of one of his student's jutsu. He had not gotten around to completing it at the time, but the theory of how the jutsu would work was sound, as was the steps he had written down as to how he thought it would be completed. Say what you want about the man, while he may have been a shitty father he was an excellent shinobi. Naruto had then taken those steps, and after a little experimentation, had concluded that the jutsu could be performed and completed it, although he had never actually tested it.

Time for some testing, and the best part was that he didn't even have to create the conditions to be able to use the jutsu first.

Naruto got up and left the stadium, going over to a nearby rooftop instead. Focusing, he then began to change his chakra into lightning, and charge and gather it in preparation for the technique. Once he was ready, he ran through a relatively short string of hand seals. Tiger-Rat-Horse-Monkey-Dog-Dragon. He then shot a deceptively small ball of chakra into the clouds above the stadium.

Once it reached them, lightning began to course through the dark clouds, as if they could barely hold back without unleashing them. Once the jutsu was fully complete, Naruto unleashed it on the stadium with a cry.

"Kirin!"

With that shout, an immense blast of lightning shot down from the sky and impacted the stadium with the force of a large meteor. The thing that came down from the sky couldn't be called a bolt of lightning, even ignoring that it came in the shape of a dragon, the sheer size of it would prevent anyone from considering it such. Indeed, those who witnessed the strike would go on to call it a judgment from God. And that would be even before seeing the damage that had occurred after the smoke cleared away.

There was no stadium left. At all. Where it once stood was only a smoldering crater, so deep that many would rather call it a fissure. No one and nothing had survived the attack.

This actually went beyond Naruto's intention. While he wanted to destroy the place and cause major damage, this was far more than he had planned. An attack like this had a chance of spooking some of the people that he had to kill and driving them underground. Instead of just being a show of strength, this could cause the enemy to panic, and panicked people tend to be unpredictable. If they freak out enough, there's no telling what they might be willing to do to save their own asses.

Staring slightly at the ruin he had unwittingly created, Naruto gave a small, sheepish chuckle and rubbed the back of his head nervously. 'Note to self, Kirin is off limits from now on. Jeez, this is just overkill.' He thought to himself while surveying the damage. Shaking his head lightly, he decided that it was time to get out of the area and turned to leave.

Taking one last look over his shoulder, Naruto then leaped away, vanishing into the evening.

A/N: Quick disclaimer, the scene with Koenig and Heller is straight from a cut scene in the game (at least until Naruto kills him).

So yeah, Koenig bites the dust earlier than the game and Guerra survives. I personally didn't like the fact that he was killed off in the game, so I saved him here. As for things happening earlier than in Prototype 2 (Koenig dying, Guerra getting attacked), that's due to Naruto's involvement. Since he showed up, Mercer's plans have all been accelerated to compensate. Mercer knows very well that Naruto is powerful, and is trying not to underestimate him. So he's trying to get everything he can off the ground in the hopes that he can get something past him while he's dealing with other things.

Plus, I kinda want to get Naruto back to the Elemental Nations, so I'm speeding up the timeline as well. I decided to drop some items that I was going to cover (they'll all happen in the background and may be mentioned in passing) just so that I can get through this quicker.

Again, please review and let me know what you guys think!