A/N: Hello everybody, I'm back with another chapter of Prototype Maelstrom, you may now scream in joy, or do what ThunderBird8950 did and start bouncing around like a little girl at the sheer badassness of my story. Well anyhow, this chapter will officially give this story over 10K words. I know it's nothing compared to some other authors who have that many words per chapter, but it's still a milestone I'm happy to reach, and it shows I'm sticking to this story to improve my writing and see how this story evolves. I'm still trying to think of a few girls for the harem, so far I have Haku (Female version of course, and in Samui's words... cool), Tenten (Girl with a weapons fetish, perfect match for a man who is literally a living weapon of mass destruction), Yugito (We all wanna see how well this kitten will play with the fox), Matatabi (Catgirl, need I say more), and Fu (... Ok I can't think of anything clever to say, sue me... actually don't, I don't have anything you'd want). Well this will be my take on the Invasion, I hope you enjoy it. And I feel I should say this now, since I know a lot of you want a harem story that doesn't have the cliche CRA in it I've found a way for a harem to work in this story without it, as to what it is you'll just have to wait and see. One last thing, you've definitely got a few questions in mind after the first few chapters of this story, and a few more questions will come up during this chapter, so I'll tell you now, a lot of questions are going to be answered in Chapter 6, a lot of that chapter is going to compose of flashbacks and dialogue, but we'll cross that bridge when we come to it. Onto the disclaimer. Last Chapter's Word Count: 2,945 words.

Disclaimer: I can't believe you jerks keep making me say I don't own Naruto or Prototype. I'm gonna go cry in a corner now.

"Bring it, punk." - Character talking

'Echo.' - Character thinking

Giberish - Anything relating to flashbacks, "talking" and 'thinking' are the same

"Foolish meatbag!" - Biju/Summon/Other talking

'I hate you all.' - Biju/Summon/Other thinking

"Rasengan!" - Jutsu/Technique

The bedroom - Location, Beggining or End of Flashback

In the Chunin Exams Stadium

Naruto deactivated his clawed form as he saw an explosion come from the Kage's Box. He looked over to see Temari and Kankuro grab Gaara and jump away with him. Looking into the stands he saw his teammate Sasuke jump off, most likely in pursue of the Suna's siblings, as well as several of the shinobi in the crowd began to dispel the genjutsu as several of the civilians in the crowd began to undo transformations, revealing them to be Suna or Oto shinobi. Several of the foreign shinobi then shunshined into the village to begin the assault. Naruto caught a kunai that was launched at him by the Suna siblings sensei Baki. Baki ran through several handsigns, creating a blade made of wind chakra in his right hand as he ran towards the black-haired Uzumaki. Baki made to slash at Naruto, who blocked it by swiftly grabbing his right arm and delivered a hard punch to the Suna Jonin's stomach, causing the wind blade to vanish. As Baki grabbed his stomach and fell down to the ground in pain, Naruto then proceeded to say, "You should know that Orochimaru isn't as much of a friend to Suna as you think he is."

Baki looked at Naruto with a mix of questioning and pain and asked, "What do you mean?"

Naruto stepped towards Baki, picked him up by the collar of his flack jacket and placed his hand on his forehead as he said, "Let me show you." A strange black and red chakra surrounded his hand as he touched the Suna jonin's forehead, and from there, Baki conciousness descended into darkness.

Flashback: Unknown location or time

Baki was standing in front of the snake Sannin, to his right was Yoroi Akado, and to his left was Orochimaru's right hand man, Kabuto Yakushi. The snake Sannin opened his mouth and said, "You remember your mission, you are to take the Chunin exams once more to further our plans, from the second exam onwards you will each have your own jobs." He looked towards Kabuto and said, "Kabuto you are to collect more data on the last Uchiha and the other various shinobi in the village. Afterwards, when the finals start, you are to cast the genjutsu to put all of the Leaf shinobi and civilians to sleep, this will act as our forces signal." Seeing Kabuto nod in understanding he looked towards Yoroi, "Yoroi, your job is simple but important, if you are able to, you are to fight the Uchiha after the curse mark has been applied to him, and use your special talents to make him draw on its power." Finally, Baki saw Orochimaru look towards him and say, "Now Misumi, your job is one similar to Yoroi's and shared by the Oto team, after the Uchiha has used the curse mark you are to fight him and see how well he uses its power."

Baki felt himself nod along with Yoroi and Kabuto, before Kabuto asked, "Lord Orochimaru, what will you be doing until the final exam?"

Orochimaru responded with, "Well it turns out your assumptions were right Kabuto, the Kazekage is having second thoughts about the invasion, and is even considering calling it off. So I'm going to have to have a 'talk' with him."

Baki felt shock upon hearing this. He knew the snake Sannin had less mental stability than Gaara, with a bloodthirst to match, so when he talked about his complications with the Kazekage, it could only spell disaster. He then thought back on the month leading up to their arrival in Konoha, the Kazekage had been acting more and more distant and short with people than usual, and if anybody so much as questioned him, the chances of seeing them again were somewhere firmly between zero and no-way-in-hell. He finally came to a conclusion he sure hoped was wrong, but he could tell he was 100% right. With that he could feel the world spinning around him and feel as though existence was fading around him.

Flashback End

Naruto released the now consciousness Baki and let him fall to the ground. Naruto looked down and said, "You saw the memories of one Misumi Tsurugi, one of the snake-pedo's little pawns. Orochimaru killed the Kazekage and took his face in order to take up his identity for roughly a month and a half in order to organize the invasion plans with Suna."

Baki stood up and asked, "How did you obtain this info?"

Naruto smirked and said, "A shinobi's gotta keep his secrets. Also if I were you I'd probably spread the word to the rest of your forces before they end up mincemeat."

"What do you mean?"

"Do you really think I wouldn't tell the village about the invasion plan? Just look around."

The Suna Jonin looked around the stadium and saw what the boy in front of him meant. Nearly every Leaf shinobi chunin rank or higher had dispelled the genjutsu, suprising the foreign shinobi who had been told that only the most skilled shinobi would be able to identify the genjutsu quick enough to nullify it, unless they had some form of warning. The Leaf shinobi had no intention of letting the advantage of their suprise element go to waste and were able to utilize it to either kill or cripple around two dozen or less of the foreign shinobi in the first five minutes. Only now were they getting over the suprise and fighting back full force, but the damage had been done and it would effect them throughout the mission. Suddenly realization struck him, if they knew about this, then they had probably strategically placed shinobi throughout the village in order to minimize the damage, they may have even dealt with the summoners in the forest to prevent the assault with the giant hydra-like snake.

Struggling to get to his feet he said to the once blonde, "I see what you mean. Orochimaru played us like our own puppets, I'll alert my comrades to retreat. If you can, would you spare those of us whom you meet before they recieve word?" He asked, thinking that his request would only be in vain.

Naruto nodded and said, "Don't worry, I intended to spare the Suna ninja, I'll either knock 'em out or capture them. I'll even be a bit generous, I'll see if I can help out Gaara with the voice in his head."

Baki's visible eye widened in surprise, here was a ninja who had his village betrayed by those who had proclaimed themselves allies, and he was willing not only to spare those who had commited treachery, but also help one of their own who had wanted to rip him to shreds not even ten minutes prior to their conversation. Not wanting to look a gift horse in the mouth Baki stumbled back into a standing position and shunshined off to find as many of his comrades as he could, knowing those who were fighting in the arena had already signed their death warrants, and were just trying to take as many with them as they could. Naruto looked up at the top of the Kage's box to see it encased in a swirling purple square barrier with ANBU agents around it trying to find a way in.

Naruto merely looked on and said, "You better survive old man, same to you Ero-Sennin. I'd hate to think that I warned all of you about this just so you could die."

He looked out in the direction of the village and saw columns of smoke escaping into the sky, smirked and said, "Well, I guess I'll let Sasuke chase Gaara for a bit then catch up to him, in the meanwhile I could go for a bit of wanton destruction." With that said he shunshined out of the arena.

On top of the Kage's box

Orochimaru was, putting it mildly, not having a good day. First, apparently someone had found out about the invasion, so several of the Leaf's shinobi had been alerted, and thus were able to plan ahead. Which brought him to his second problem, because his enemies found out about the genjutsu they were able to plan ahead for this and use the surprise element to kill off several of his forces. Third, his former sensei, the Sandaime, had called his former teammate, Jiraiya, to aide him by hiding with them in the Kage's box with them using one of his famous camoflauge jutsu, waiting for Orochimaru to make his move. This caused a major problem, he could handle his sensei since he was no longer in his prime, and he could handle his former teammate on a one-on-one match, but to handle the two at the same time would require powerful help, which brought him to his next problem, his attempt to revive the Shodaime and Nidaime Hokage had failed miserably. The pervert had used two strange seals, that he sensed had some of the Kyuubi's chakra in them, that were able to corode the forms of the previous Fire Shadows and even the seals that bound their souls into their ashen forms, leaving only the corpses of Zaku Abumi and Kin Tsuchi who were the human sacrifices required for using Edo Tensei. So yeah, not really a good day for the snake-pedo.

Right now he using the famed Kusanagi blade to block a powerful blow from Sarutobi's bo staff of the monkey king, Enma. When he was distracted Jiraiya had aimed a Frog Kata at his side, causing a few of his ribs to break. The snake Sannin recoiled in pain and jumped away from his former associates, going through several handseals he used Wind Release: Great Breakthrough, which launched the two away from him. Trying to catch his breath, too late did he realize that Jiraiya and Sarutobi had substituted with Shadow Clones effectively avoiding the jutsu, and unknown to the snake Sannin they had each thrown a kunai with a seal tag wrapped around the grip. Orochimaru's eyes widened, knowing that he couldn't avoid them he raised his arms in front of his chest, which would prove to be his biggest mistake. One kunai had hit each arm, and as he bit back a scream he was about to pull out one of the kunai he suddenly felt an immense, burning pain in both of arms. He tried to lift up his arms to see what was wrong with them, but found that he could not move them, and trying had only caused the pain to increase. Looking down he found the seal tags on the kunai were glowing with an evil red chakra, and from the points where the kunai were stuck in his arms, they were darkening and turning purple, as though his arms had died. In shock, he asked, "W-What have you done to me?"

"In all honesty I'm not entirely sure. We got the seals and those kunai from the formerly blonde gaki. You know, the same one you had the oppurtunity to kill back in the Forest of Death, but didn't because you thought he wasn't even a threat to one of your failed experiments," replied Jiraiya with a slightly mocking tone at the last part.

The Sandaime glared at Orochimaru and said, "I've always regretted not killing you all those years ago, you do nothing but cause pain and misery upon every living thing you touch, and you feel no regret for what you've done. And I must admit, I look forward to when you finally die and have to face judgement."

Orochimaru cursed under his breath and signaled with a flare of his chakra to his subordinates the Sound Four to evacuate. The four dropped the barrier and quickly used several powerful smoke bombs to cover the entire rooftop in a thick cloud of white smoke. Utilizing this oppurtunity, they grabbed onto their boss and jumped away. The Sandaime, Toad Sage, and several ANBU tried to follow in pursuit but were stopped when one of the Sound Four, who had six arms spat out several, large, white webs which they had to avoid, which gave the red-headed member an oppurtunity to cast a genjutsu to create several fleeing images, allowing them to escape. As they landed on a nearby rooftop Jiraiya cursed under his breath and muttered, "I can't believe I let him get away again."

Sarutobi looked at his student and said, "It's fine, thanks to the seals on the kunai we were at least able to disable his arms for a time. Which raises a few question about your godson that I hope he'll answer."

Jiraiya nodded, both of them clearly remembered how only two weeks ago someone had appeared in the Sandaime's office and told them of Orochimaru's invasion plans and gave them the seals they used against Orochimaru.

Flashback: Hokage's Tower, two weeks ago

Jiraiya had just arrived in the Hokage's office to speak with his old teacher. Walking up to him he asked, "So teach, what did you call me here for?"

Sarutobi raised an eyebrow in confusion and said, "I didn't call for you. You already told me about your plans to train Naruto two weeks ago, and you already gave me your spy reports. Why would I need to call you?"

Jiraiya got a confused look on his face and was about to ask another question before he and his old teacher heard the sounds of bodies hitting the floor in the room. Looking around, they found the four ANBU members that were stationed in the room were all unconcious on the floor. Sarutobi quickly removed his Kage robes revealing his battle armor while his student was already molding chakra, preparing to fight. The two were standing back to back until they heard a mocking voice, "Wow, you two need to calm down, high blood pressure's not good for people your ages."

They looked around and saw someone neither recognized sitting on the window. He looked to be in his early teenage years, with pale skin, his entire attire was mostly black, as was his hair, save for one red streak in it, as well as icy violet eyes. He looked at the two of them with a look of amusement and continued, "Also, little note to you old man, get better bodyguards. I may have had the element of surprise, but I shouldn't have been able to knock out four members of the Leaf villages supposed 'elite' special forces."

"Who are you," the aged Kage asked, still on guard should the stranger try to make any hostile movement.

The boy merely gave another amused smirk and said simply, "Possibly your best friend right about now."

The two older shinobi gave a look to him elaborate further. The black haired youth merely gave an exhausted sigh and said, "If you want specifics, such as a name, I'm afraid I cant give them to you yet. I've got way too many plans to be giving out my identity this early."

The two kept their guard up despite the fact the youth had not made one motion to even so much as get down from the window sill. The black haired youth gave a theatrical sigh and said, "Oh, how far the Leaf has fallen, a man once heralded as the Kami no Shinobi can no longer tell when his own village is in danger."

The white haired duo's eyes widened in surprise before Jiraiya asked, "Let me guess, Orochimaru's behind it, isn't he?"

The boy merely rolled his eyes and said with sarcasm practically 'dripping' off his voice, "Wow that's amazing. How'd you figure that one out."

After that the black haired youth stepped off the window sill and onto the office floor. Placing his hands behind his head in a sign of peace he began to elaborate further, "As the super pervert there said, Orochimaru is indeed plotting to destroy the Leaf. But the thing you two don't know is how he plans on doing it, and if you'll give me naught but an hour or so of your time I can explain further, and possibly save a lot of lives."

The old duo looked at each other before lowering their guards slightly and saying, "We will listen to what you have to say, but make one hostile movement and your life shall be over."

The unidentified boy smirked before lowering his hands to his sides. For around an hour he began to tell them of Orochimaru's plan in great detail, how he had positioned several of his lackey's throughout the village, how he had taken the Kazekage's identity to get the Suna shinobi to aide him in the invasion, how he planned to use a powerful genjutsu to make it difficult for the shinobi in the Chunin Exams Stadium to fight back, how he planned to use the Shukaku vessel to cause widespread destruction to the village, how he was going to place summoners outside the village walls to summon a giant snake to attack in conjunction with Shukaku, and lastly, how he planned to assassinate the Sandaime using the Nidaime's kinjutsu to resurrect the dead. By the end of the little speech, not having sensed even a single lie, the two were completely shocked, they had never thought that Orochimaru would actually make such a bold attempt on the Leaf, and if they had to admit it, the two of them would have never seen it coming.

While the two were still stunned, the unknown boy withdrew four seal tags from his hoodie pocket and gave them to the Toad Sage. Pointing to the two in his left hand he said "The two you have in your left hand are meant to deal with the kinjutsu, don't worry about the specifics, just roll with it." Pointing to the right hand he continued, "These two are meant to strike an enormous blow against Orochimaru. As for what they do, well, let's just say if I were you I'd try to hit either his chest or his arms."

Looking over the seals, Jiraiya could tell that these were very complex seals, and whoever made them must have taken around two weeks to make them all. As to what they did, he couldn't tell, the designs were unfamiliar to him, and the ink was different as well, instead of the usual black, it was a bright red color. Jiraiya looked up and asked, "I know you don't want to answer this, but who are you, and how did you find out about this?"

The boy looked at the two and replied, "I already said I can't tell you who I am yet, but I can gaurantee after the Chunin Exams are over, you'll know exactly who I am. And as to how I know, well, you talk to people to gather your info, I have less... gentle methods of finding out what I need to know." Giving a dark chuckle at the mention of his methods.

The two older shinobi looked at each other before the Sandaime gave a respectful bow to the boy and said, "Thank you, you have no idea how much suffering you've spared."

Jiraiya noticed the boys scowl, as though he hated the idea of sparing the villagers of suffering was one of the last things he wanted to do. He quickly recomposed himself before any questions were asked and with one last comment said, "You'll know where to find me when the Exams are over, and from there I'll answer your questions."

With that he ran towards the window and jumped out, leaving the two behind. They briefly considered chasing after him, but decided against it. The two looked towards each other and with a nod decided to go home, they would have a lot of work to do in order to minimalize the damage from the invasion. And, somewhere deep in their minds, they could tell that there was going to be a massive shift in this village. As to what it was, they didn't have a clue.

Flashback End

They recognized the form Naruto took after being hit by Neji as the same man who had warned them of the invasion. This of course answered the question they had during the meeting concerning who he was, but raised quite a few questions. Like how did he obtain the abilities he demonstrated earlier, how long had he put up that mask, how was he able to make such complex seals, and how did he find out about the invasion? The two heard an explosion off in the distance and decided that they would ask him later. Each of them nodded at each other and shunshined, ready to protect the village.

Scene Change: Konoha Village, near the gates

Naruto was on edge of a building overlooking the village gates, below Konoha shinobi were facing off against the shinobi of Otogakure and Sunagakure. Smirking to himself Naruto backed up before he ran to the edge and jumped up into the air. At the apex of the jump he got a look of concentration on his face as tendrils began to writhe around his right leg and then he began his descent. Hitting the ground, a shockwave rang out from the point where his foot hit the ground, causing several of the foreign shinobi to be flung back, and the ground beneath his feet to shatter. Several of the Oto shinobi recovered quickly and charged at him. Naruto merely rolled out of his standing position to one of the charging shinobi and uppercut him into the air, a red light trailing behind his fist as he swung it. Quickly pivoting on his feet he kicked the Oto nin charging at him from behind, noticing several of the foreign shinobi trying to surround him, he smashed his fists together launching them away from him. The Konoha shinobi that had been stunned by the arrival of the Uzumaki quickly shook the cobwebs out of their heads and began to resume their fight against the foreign nin. Naruto saw another two Suna near him trying to get back up off the ground, rushing over to them he quickly chopped them on the neck then tossed them away from the main battle area. Turning back to the battle at hand he rushed towards two Oto nin that were attacking from a distance with shuriken. He smashed his fist into the skull of the Oto nin on the left, effectively ending his life. While he was still in shock, Naruto grabbed the Oto nin by his neck and lifted him up into the air as he tried to pry apart the Uzumaki's iron grip. Naruto looked up at the struggling man in his hand, gave him an evil smirk and said, "You know, it's remarkable for you to help out a village that's not even your own."

Naruto then drove his right hand into the chest of the Oto nin, causing him to scream out in agony. Naruto dropped the Oto nin onto the ground where he began to clutch his chest and writhe in unbearable pain. If anybody looked close enough they would notice a strange black and red aura leaking out from the hole in his chest. Naruto smirked his usual evil smirk, drawing back his leg, he kicked the Oto nin into a group of his friends and shouted out, in a humor filled tone, "Don't forget to write!"

As the Oto nin collided with the group, tendrils sprouted from his chest and wrapped up the group. Several more tendrils began to sprout out from the group and began to grab everything in sight, fallen concrete, dead bodies, fallen water towers, and everything else you'd find on the battlefield, and pull it towards the group, causing it to collide with them with incredible crushing force, turning them into nothing more than a big mess of paste. Reveling in the carnage he didn't notice one of the Suna nin sneaking up behind him with a wooden board, about to strike him. Alas, it was not meant to be, as he made to swing the board, several senbon hit him in the neck, paralyzing him. Naruto looked down at the shinobi behind him and noticed the senbon needles in his neck, eyes widening he looked around until he looked up at the top of the villages gates and gazed at a cloaked figure standing on top of them. Noticing the figure he quickly ran up the side of the gate to the top and walked towards the figure. The figure looked towards the black haired Uzumaki, smiled a gentle smile, and said in a beautiful feminine voice, "Glad to see you dropped the disguise, but I thought you were going to keep it up a bit longer."

Naruto gave a sheepish smile and said, "Well things didn't exactly go as planned, and last time I checked you didn't really seem to mind this form."

The figure merely smiled again and removed the cloak, revealing a gorgeous feminine figure, clad in black shinobi sandals, tight black jeans, and a black tanktop with icy blue tribal marking on the back. Her face was, for want of a better term, angelic, with smooth, pale skin, doe brown eye that seemed to have an almsot icy appearance to them, her hair was black, with two bangs framing her face, and the back was held up in a white bun holder and two pins. She gave her own sheepish smile and said, "True, all too true. But I'm happy to see you love."

Naruto closed the distance between the two of them gave her a kiss on the lips, hugged her close and said, "Me to Haku. I'm so glad to have you back."

The two seperated as Haku asked, "So, are you gonna tell me what's going on, or are you just gonna let me guess?"

Naruto responded with, "Short version, Suna and Oto are invading Konoha because of a plot of Orochimaru's design. I told the Hokage about the plot, a bunch of plans were made, and now here we are, standing on top of the village's gates." He gave a smirk at his humorous shortening.

Haku rolled her eyes and asked, "Well, anything else I should know?"

"Yes actually, Shukaku's jinchuriki escaped into the forest along with his siblings, currently they're being pursued by my teammate Sasuke, and I've gotta go save him before Shukaku takes over and kills him. And if you'd like you can help out here in the village, just remember this, capture the Suna nin, and the Oto nin, well, you can do whatever you want to them."

Haku nodded and was about to jump into the fray, but paused for a moment before kissing Naruto on the lips and saying, "Consider that a bit of motivation, come back and we'll do a lot more of that and then some."

Saying the last part with a seductive purr, she gave one last saucy wink and jumped off the gates and into the battle. Naruto stood there with a bright red blush on his face, in his mindscape Kurama was laughing his ass off. Eventually he recovered and looked out at the forest surrounding Konoha, sighed and said, "Now I gotta go searching through this massive freaking forest for a psycho with a demon in his head who wants to tear my head open. Joy."

With that he leapt off the gate and into the forest, starting his search for the Shukaku jinchuriki.