Disclaimer: I DON'T OWN NARUTO, otherwise (cannon) Sasuke would suffer Bloody hell.
Nor do I own ANY cross over however slight it may be.

Be careful, God is watching.
In a street blacked by night, please link our hands together.
Even if I'm by myself and far away, He can always come find me.
He comes to teach me everything He knows.
Even if I should no longer remember,
He will teach me over and over
But what should I do once I know everything?

Chapter 6:
The truth behind all plots

Naruto's Mind scape

Kyuubi was worried, over the past 5 years the events that triggered it's conscience, so to say, had finally finished, and the results to say the least were intriguing; It had taken the form of a middle aged woman, with long white hair, her body fully developed and was probably, arousing? was the word? she thought so, in all truth she didn't knew what to make about how she looked, much less about the memories of all her actions up to 2000 years prior her sealing. In those memories she found herself more and more intrigued, the further she went into the past, the more she felt like she chose something wrong, and there was one point where she felt like her head was missing a body, or was the body was missing a head?, she didn't knew, but all the knowledge the had been previously ignored, under the wraps of infinite rage and hatred for humans, was now free to roam through the great creature's mind. The past year; however, she felt her host's mind become more and more confused, like there was some kind of pressure somewhere, and she sought to cure him of this, she hoped that under time she could bring him the comfort that he seemed to need.
She soon discovered that her chakra could heal the boy, and even augment his body. But during a shopping trip Naruto made for a bit of food he was poisoned, and that's when she discovered something that took some time to comprehend: she cared for the boy, and when she found out that his body was all but immune to poisons of all kind, that his blood was so used to such a substance that his blood was poisonous to others, that she wept for the first time in what felt like eons. She didn't knew what was happening but she did knew that the longer she spent with the boy, the more she would be able to understand and help him.
That's when the third change came, her chakra had been restless in the time she had been sealed, but when the boy linked himself to the planed infusing himself with a tremendous amount of mako, and when he first used Nen, her chakra reacted, it changed to something more powerful, more controlled, and above all, it seemed to evolve, it was adapting Naruto's body to do the same, and that's what brought this worry. The boy had been focusing all his three energies into his eyes and brain in a limited amount, but that's were all went wrong:
His body had already adapted to the change her chakra brought to him, and when he tried to augment his eyes his energy started modifying his genetic code to meet his need.
Then her chakra reacted and she puled Naruto from his conscious mind into the room where she was kept, watching as the surroundings changed from a gigantic cave to what seemed to be a cluster of stars with her cage being morphed into a nebula.
"What do I do?"

While this was happening, Naruto was in his own conflict, he was getting memories from things he wanted forgotten and that he had forgotten for good, he knew that he wanted revenge but he also knew that it would leave him without any other goal. He was fighting his darker side, trying to get a reign of him self before he was consumed by his rage once more, then his fight stopped and he was pushed into his memories of when he locked up Sephiroth:
Flashback:

The day had started like any other, but for some reason, Naruto couldn't get a feeling of dread from his navel, like there was a terrible doom approaching. He shook himself and started reading again, he had to take the most out of this chance with the forbidden scroll he had taken from the Hokage tower. He sneered "How utterly foolish, they give me instructions on what to do and believe me too foolish to take this chance for revenge" He was still driven to take revenge against the village for everything they had done to him, he had finished practicing the curse seal theory left by Orochimaru and was pocketing the copies when he heard a scream "Naruto! what do you think your doing stealing the forbidden scroll!?" The encounter was cut short when a maniacal laughter filled the clearing as they both turned to see Mizuki jump through the foliage with two over-sized shuriken strapped to his back "Mizuki! what's going on here!?" "Heh, isn't it obvious? the truth must be told!" Naruto had to suppress the urge to smirk right there. He looked to Iruka, who was still in the tree, and noticed the worry creeping all over his face, and then he sprinted in a mad dash towards the Chuunin.
He was knocked over Naruto however as Mizuki blew him off with a justsu "Naruto! do you know why the villagers despise you?" "Mizuki No!" Naruto however was getting amused by the pitiful attempts at stunning him "The truth is that, twelve years ago the Kyuubi wasn't killed as everyone thought, but instead it was sealed inside a new born baby, and guess what! it was you!!! You are the Kyuubi!!!" Naruto then froze out of amusement; they believed he was the demon!? That was laughable, hell it had to be the most piss poor excuse he heard, not even the other jinchuuriki had undergone that, at least not until they attacked and killed everything around, yet this maggots claimed him to be a demon because they couldn't find a better excuse to beat him up. He no longer knew whether pity them for they foolishness or wipe them out to save the trouble to God.
He was barely aware that Iruka had jumped in the way of the shuriken Mizuki had launched at him, and when Iruka told him to run with the scroll he only nodded and ran. "You know Iruka, I was going to kill him first, but since you seem so attached to the demon, you shall go in his stead!" with that he launched a volley of kunai straight to Iruka intent on killing him, but was stopped by Naruto who blocked them all with his own.
"Mizuki... you call me a demon, but tell me, what IS a demon?" "HAHAHAHAHA, You don't know? a demon is a beast that kills by instinct and without feelings, such is it's nature!" Naruto was more pissed than anything now "Then what makes them different from you soldiers?" "What?" asked Iruka and Mizuki at the same time "What makes them different when the shinobi kill without remorse, when they are ordered to kill and they believe they do it for the right reason! when they kill their emotions and go to slather everything on their paths! isn't that what you describe as a demon!?" "But.." "ISN'T IT?!"

He had to wait for his answer as the time came to a stop and a cold feeling filled the place, suddenly the clearing faded into a black room with a glass platform on the floor, the glass was about 15 feet in radius and was perfectly clear, glowing with a white silvery light, he then turned to see Sephiroth-sensei standing in the other end of the platform "What's happening sensei?" He got a glare in response and he idly wondered what was happening once again "You were supposed to be the new son, the new harbinger, but I won't let you take the place of mother, I'll take over your body and be the new Dark harbinger! And with this new body I shall do it!" Naruto then grew a worried look in his face, he dreaded the day this would happen. He noticed that he was wearing his knight "armor" (will post image*).
He knew that every second he wasted was another second Sephiroth used to his advantage, he saw him summoning his masamune to his hand and he responded by summoning his own sword. The sword had a 24 inch long handle, and had a blade sticking out on each end each half as long as masamune.
There were no words exchanged as the two charged each other at speeds that dwarfed sound. They clashed in the middle of the platform and began exchanging blows at the speed they clashed mantaining themselves midair with the strength of the slashes, the recoil was tiring Naruto but he could see that Sephiroth wasn't even trying.
They finally slowed down and the two fell to the ground while circling each other looking for an opening keeping their guard up, Sephiroth saw one and charged Naruto at top speed who could only block the many slashes while Sephiroth appeared behind him and rose to the air while calling "Heartless An-" but was cut short when Naruto shot towards him and sludged him in the Face with a Nen powered punch, Sephiroth growled and slashed upwards in an attempt to cut Naruto in two while he descended, but he blocked and began exchanging blows once again. Finally they broke and Sephiroth called "Firaja!" and a colossal fireball shot out blocking the view with it's sheer heat and brightness, while Naruto launched newest technique "Chaos Energy!" The attack was absorbed into a glowing orb in Naruto's arm and he immediately raised his sword to block the attacks from Sephiroth.
He was sent forward by a firaga blast from Sefiroth, who had gotten behind him when he parried the multi-slash attack. His armor, however, protected his back from harm, and he rolled away when Sephiroth stabbed his sword into the panel cracking it, and the light burnt him away from Naruto, who saw this and capitalized on it by rushing top speed towrds Sephiroth who was already rising his sword to block, and was stunned to see Naruto divert the attack to the ground and ran straight through the crystal, which collapsed all under Sephiroth, when he used his Nen. "ARGHHHH!" Sephiroth roared in pain before vanishing in a swirl of darkness but his voice remained "I'll destroy you, You won't take mother!" Naruto stayed standing there for a few minutes before a voice whispered "Don't loose your light, it's all you have"
"My light? MY LIGHT!? there's no light to me, all I ever was, all I've ever been to those I cherished, was a Demon, a beast of destruction, nothing more, nothing less" The platform disappeared and so did his sword and armor.
His arm, however, still contained the power of the firaja from the battle. He grew aware of the time returning to it's normal state of and the surroundings returning to normal, as if nothing had ever taken place, Mizuki was moving once again his words doubtful
"What is a demon? what is a shinobi? what... am I?"
Iruka was speechless, Naruto accepted the truth with responsibility and used it to put reason in others.
"What about you? what are you?!" Naruto looked down and said "I'm a weapon, or at least I think so... and I'm a soldier, and I am determined to take back what's been taken from me!"
Mizuki took this as a threat and attacked launching a barrage of shuriken "No! you won't lay a finger on them!" but was stopped when Naruto unleashed all the energy in his arm, melting everything in the line of fire. Mizuki fell from the paradox he was facing and whispered " What are we?" he fell unconscious from the shock. Naruto turned around and created a shadow clone to help Iruka stand again and asked "What are you going to do now? Finish the demon? if so, then there's nothing stopping you, I'm already exhausted from the blast and the clone" Iruka was confused, why would Naruto think that? "No! you are not a demon! you are Naruto Uzumaki! you're my pupil and my family!" "Why... why do you care so much? what did I do to deserve such?" "You proved time after time that it was worth the struggle, you give hope to shinobi who by all accounts should have retired, your willpower is a thing of legend in the ranks! You are the thing that's kept me believing in something better!" they kept talking till sunrise when the left for the Hokage tower to explain the happenings from the night, Iruka accommodating Mizuki in Naruto's back.
Family, that was the word that marked that day.

End flashback

Naruto opened his eyes and found himself in his unconscious, he turned around and found it to have changed into the core of a nebula with stars of all sises and colors shining in the distance. he noticed movement in the front and moved to see himself behind a jail made out of stardust "Who are you?" the other Naruto turned and his face morphed into surprise "So, you finally came, after a year of being separate beings, though I can tell your presence here is not voluntary, what happened?" "That's what I would like to know, and you still haven't answered the question"
"True, I'm what you fear, the embodiment of the things you've grown to hate within yourself, your darkness, in a way" "My, darkness? how? when?"
"Yes, as for how, it was during the battle with Sephiroth when you used the light beneath the panel to drive him back, that we were completely separate, but it began with the mako surgery, that pretty much answers the when and how"
"But why are you here if we got *separate* as you say, wouldn't you be a separate entity from me?"
"No, we were always one, but we were separated by that light, why, I don't know, but I do know this, we need to be one again for you to be complete"
"But if what you say is true, then I could plunge deep into my anger and Konoha would suffer, my friends and family!"
"That's only if you want to, the fact remains, we're never be complete until you acept the fact that since you did the mako surgery you changed, if you don't accept it, you'll never be whole, and if you continue to deny yourself, the time will come when you're forced to, and believe me, it will be beyond painful"
"I don think so, but tell me, Kyuubi is really a female?"
"Yes, but she wasn't conscious of that fact until 5 years ago"
"Why?" "It was during the attack you suffered in which you used the double core henge fuuin, her chakra is always evolving to make her impervious to the things that defeated her before, and in some cases it gave her knowledge"
"How does that explain her consciousness?"
"The trauma that affected you forced her chakra to make a way to cope with the feelings pouring down to your subconscious, as a raged mind could not stand the stress such feelings brought"
"So, have you met her?"
"Yes, but she isn't the bloodthirsty beast she was, she has been cleared of her rage and made complete"

With that Naruto left to find Kyuubi, but what he found was nothing like he expected. He understood that it was a she, all right but never expected to see a 23 year-old woman that was the epitome of beauty, with a soft skin, a soft peachy color, her legs strong and firm, her breasts like a matured fruit that stays firm in the harshest of winters, her face more beautiful than any artist could ever imagine, her hair was a platinum blond that was almost white in color, and her eyes a honey color that shone through the darkness like a lantern guiding those who searched for her embrace. (I refuse to describe her as a piece of meat)
The nebula that was her cage bathed her in a blue light that made the image an immortal memory on his mind.
Kyuubi stopped looking arround when she noticed him in front of her, and saw the mesmerized look on his face, she understood the reaction but asked something that stunned Naruto that much further: "Am I really that beautiful?"
He sputtered his response "O-Of course you are! y- you are the sight I could watch and die content!" She actually blushed from the comment and asked "Are you okay now?"
"Yes, thank you, but what happened?" She shuffled nervously in her Nebula and said: "Y-you were trying t-to make your sight better r-right?"
"Yes" He felt unnerved by the fact she was nervous in his presence "W-well, my chakra, e-evolved and it changed yours a-as well"
"So it changed me, how?" "It adapted your body to make it improve itself to m-meet your needs" Naruto's eyes widened at the implications of such a statement, the chance of getting a new kind of eyes was beyond what he had hoped for!
"A-Are you okay?" she asked again seeing his eyes widen with excitement "Y-yes! this is the best news I've had! thank you!" They both didn't realize it but they were developing a link that bound them beyond the seal even if it was only a little bit.

Konoha, training grounds
6:00 a.m.

The day had finally made it's break from the night, the sun was bathing the trees around the clearing where a blond boy was resting, the boy however had a remarkable build for someone his age. His body was muscled and built for speed and strength. Naruto woke with a groan, he was sore in every place imaginable, and his eyes hurt the most.
He lay there on the ground and watched as the sky turned a soft blue, there was some birds on the sky, Naruto remembered the words his *other* had told him, wondered if they were true, or if the price for hope was really so high.
He sat up and reflected on what he had learned from Kyuubi, and tried loading chakra into his eyes
Nothing, his eyes were what they had been for the last year, he sighed and stood up "Well if I spent the night Here I will at least make sure it was for something"
He got up and charged the chidori, he was facing a boulder that was half a mile away and charged at top speed, he covered the distance in 5 seconds (about 160 m/s Metre per second) , but that was enough to realize that the tunnel vision was no more, so after removing his hand from the boulder, he ran a full mile in the opposite direction and noticed that he could see the energy flow in all living things around him, he then turned his eyes to the voices up ahead and noticed his team reuniting in the bridge outside the clearing.
He than saw that their shadows seemed to be moving with them, almost as if telling how they were going to move the next second.
He left that for later and went to his apartment to change into something cleaner.

By 8:00 in the morning he had already returned to the bridge
"Naruto! You're late!" "Sorry I was training until late at night and fell asleep in the clearing over there and when I woke up I saw you here and I went to change" "Yeah right!" Naruto sighed and decided to leave it alone. "Hey Naruto" "Yes Sasuke?" "What's up with your eyes?"
"Why?" "I saw them shifting colors" Naruto went to the river, saw his reflection and gasped when he saw his eyes. His teamates hearing the gasp walked over to see what was it and saw his eyes, they gasped at what was there...

Kakashi was returning from a briefing from the Hokage tower to the bridge when he noticed his students all watching something, when he walked closer he noticed the confused looks in Sakura's and Sasuke's faces while Naruto looked like a boy on Christmas.
"Oi, what's happening?"
"S-sensei, look at Naruto's eyes" Said Sasuke whose face held hope within all the confusion
He walked over and asked Naruto to turn around, he did so, and when he saw his eyes the breath left him. For Naruto's eyes had changed, his pupil was now a thin cross that almost separated his iris in 4 and in the space between the lines there was a coma, making his eyes look like a 3 colored Sharingan.(*)
"How is this possible?" "I don't know, when I woke up this morning I tired practicing the Chidori and the tunnel vision was gone, and I can see the energy flowing in the three of you"
Sasuke was confused "It resembles the sharingan, and it even has one or two aspects of the sharingan, but what does that mean?, a lesser branch?, what does it mean?"
"Naruto, if this is a prank I'm going to send your ass to the moon and back!" Screeched Sakura unwiling to accept that a "Dobe" was related to her Sasuke-kun
"N-no it isn't a prank I can't feel any genjutsu on his eyes"
Kakashi, who had remained quiet, said: "The Hokage needs to know about this development"
The team nodded each wondering the cause of such changes, and what would they mean. They had arrived at the tower by 8:30 and the Hokage made them a hasty appointment to see what was so urgent.
"Haokage-sama, there's something you need to see" "What is it Kakashi?" "Sir I think Naruto has developed a new kekkai genkai"
"How did this came to be? Naruto, step forward and state the nature of the kekkai genkai"
Naruto did as he was told but shared a bit of information that he had safeguarded till now "...Apart from what I have told you there's also a feature that I was testing before I mentioned it, the eyes seem to track the movement of multiple targets and feed me with the possible paths they may take, they seem to be capable of locking on a single object making the tracking of He/She/It easier"
Yuukaido was silent for a moment but then said "I want you to go to the hospital to have a sample of your blood taken, you may request it form Towairiato Hana"
"I get to see Hana!" Naruto had grown fond of the nurse ever since the attack all those years ago
"Who is this Hana?" Asked a curious Sasuke "Maybe, just maybe I can ask her to..." "She's a nurse that I befriended some years ago"
Sakura was confused, what did all this mean?, what would change? she was going to talk with Ino as soon as they left for the day...
"Also, whatever was spoken here is to remain here till said otherwise, Is that clear?"
...and Sakura's hope was shot down with that line.
"Yes!"

Konoha Hospital
9:00 am

"Hana!" Hana turned to see the boy she had helped take care of for the las years, and smiled at his face, but noted something amiss with his eyes.
"Naruto! good to see you! How you're doing?" Naruto actually bounced towards Hana, he was always happy to see her, she was one of the very few people he was open around "Well I came to have a test made, but I have to make it in private" Hana understood and procured a set of keys for the nearest test room available. Once they had arrived she spun around and said "Okay, what's the test all about and what's up with your eyes? why are the flickering?"
Naruto got confused and went to the nearest mirror nearby, he saw that his eyes were changing in appearance... His iris was a solid emerald, the pupil had taken the shape of a 3'd infinite symbol that was spinning slowly in his eyes (will post image:) Hana was by his side and saw the eyes and couldn't help but be marveled, the eyes seemed to show all truth and it made her think they could see into the future.
"What's that?" "This is why I came to you in the first place, the old man needs a sample of my blood and a test confirming a bloodline, or rather a dojutsu" Hana nodded and went for the needle and container needed for the procedure.

While that took place Sasuke made towards the clan record and asked for an appointment with the director of the wing "Uchiha-sama, it's good to see you're well"
"Yes, Tank you, now, the reason I came here was too see if it was still possible to run a test on my clans blood samples"
"Yes of course, but the most it could be done would be checking similarities on your clans notorious genetic aspects" "The bloodline" "Yes, I hope that will suffice?" Sasuke seemed to think it hard and long, he gave his answer, he needed to know if wat had happened was becouse of heritage or something else, after all new bloodlines don't pop out of nowhere.

The next day the council was in a heated argument over the results of the blood test performed by Towairiato Hana. The civilians present were displeased by this developing as it could give some sort of leverage on Uzumaki's part, and that wasn't good for their plans, even more so if the boy claimed his family's money before they could siphon it into a dummy bank.
The Haruno head was seriously considering a more aggressive action, and the boy was the only thing that was in the way, Sarutobi would be taken care of and his councilors were dead or dying, so all that remained was taking care of the boy, as soon as the boy was out of the path they could sell the Namikaze's property as it was stated in Konaha's law for idle property, the techniques would go to their seal masters, the best money could buy, and they would train their underlings, with their positions the Haruno and Hayashi clans would ensure that the money went to the people that supported them in the militia and buy foreigner soldiers and supplies to their cause, and when ready they would place evidence of treason in the Hyuuga just like they had done with the Uchiha. Then things would get chaotic in the political and social plane and when the time came the two clans could reveal the full organization they had formed in the underground and take rule over Konoha.
But that plan came crashing down in a matter of minutes when it was discovered that the boy had a bloodline, once this got out to the ranks his backup plans would be blown to hell and the Towairiato warlord would have his ass for braking his part of the deal, what was worse he had a leak a few months ago and he had lost a chunk in his forces when they fled to the Hokage in exchange of political asylum.

Right now the Hokage was in his chambers listening to the discussion through the surveillance equipment he had installed after the assassination of his ex-teammates, and he readied himself to go and quench their thirst for answers before they said dangerous things.
The report from Hana was nothing short of amazing, it seemed that the bloodline was evolving even as the blood was taken, it seemed to be searching for the perfect way to fulfill the needs of the user, which needs remained unknown, but he was sure that Naruto could answer that in a few minutes in the council chambers.

Half an hour later Naruto had arrived to the place and sat down in the chair to answer some questions about the new eyes, "Uzumaki Naruto, Member of the Shinobi ranks under the service of the Hokage, rank Gennin, do you know why we called you here this evening?"
"Yes"
"Good, then please answer these question, When did the change in your eyes made itself known?" "During training"
"What kind of training?" "Speed training"
The council member scribbled some notes down in a notepad and proceeded "Can you tell us how did the eyes developed in the period between that day and this meeting?"
"Well, they first allowed me to see everything ahead of time, and I could see the energy flowing in the living around me, the eyes looked like a cross with comas in the spaces" This was met with muttering in the council, once again the man noted something in the notepad and asked
"Is there anything else?"
"Yes, after that, the slow-mo was even more pronounced, and it even predicted actions of others, but I could no longer see the energy in others, instead I began to see lines in everything around me, and everything I saw I suddenly knew everything there was to know about"
"How so?" "Anything I saw, I knew how to make or how it was composed or even how to alter it to make it function better, the eyes then remained the same in appearance, with the pupil surrounded by a tree pronged infinite symbol"
"If you could draw the symbol please?" Said the man handing Naruto a pen and a sheet of paper.
He drew the symbol and handed it to the man.
"Is there anything left to say about the abilities of this new eye?" "No sir"
"Good you can leave"

Sasuke had just received the results he had asked for after a grueling week of wait and driving himself to the ground in training to avoid thinking of the implications of a positive result.
He drew a shaky breath and opened the envelope, he unfolded the paper and began reading, at the very end it listed:

Itachi Uchiha: Bloodline origin positive

Sasuke Uchiha: Bloodline origin positive

Unknown source, a.k.a: "Eye": Bloodline origin positive

Side notes:

The last sample was taken recently and while the blood presents some anomalies to a standard Uchiha samle the bloodline gene remained the same and it seems to proceed from the same genetic source. In other words, the last batch has a bloodline that came from the original user. research is recommended.

Sasuke was speechless, he didn't knew how to react, there was another with his blood, it could be very well his best friend and someone that was willing to do good without looking for reward when it came to a friend. Maybe there was a hope in the darkness he was thrown in by his brother, maybe there could be light, maybe he could find a family.
The very next day he would be beginning a new goal, and he hoped that it wouldn't shatter in his face like it did with his brother.

An: Hope you like it and here's a link to the symbol in Naruto's eye: www multichannel com/contents/images/INFINITO_Color_Logo_3x3_30 gif
Just put the dots where they belong and an extra one before gif.