Author's Note: Hi guys its been a while since I updated my other story but I think I need to rewrite that story but for now here is my Naruto/Negima crossover this is a Negima!Neo xover since Konoka and Setsuna are in good terms without further adeu here is the story.

Negima timeline:Konoka and Setsuna -15, Naruto - 19

Flashback: Konoka and Setsuna - 5-8, Naruto: 9-12

Naruto's flashback : hokage still alive - 5 hokage died - 6


Chapter 1: Konoka

"Se-chan hayaku!"

"Chotto matte ojou-sama." The small bodyguard chased her friend/charge as both were running though the forest on the north side of the compound. Though the girl with brown hair was already breathing heavily she kept on running towards their destination as if her very life depended on her showing her best friend what she saw on the clearing the day before. As the brown haired girl neared their destination she slowed down to a jog and finally feeling the effects of exhaustion as she reached the clearing with her best friend close behind. The two walked towards the clearing, Konoka excited at showing her best friend her discovery while Setsuna was more cautious with her approach of the relic her ojou-sama found.

"Se-chan look!" The smaller girl pointed at the large cylindrical object, upon both girls' closer inspection the object was made with an unknown metal but there appears to be certain areas of the object made out of glass.

"Please stand back ojou-sama." The other girl went to bodyguard mode as she went infront of the other girl and surveyed if the object was any threat. The brown haired girl was curious though as she wanted to see what is inside the container, she sneaked on the other side of the container to avoid her bodyguard. The princess slowly rubbed the glass area of the container with her kimono sleeve, only for her eyes to widen as she saw what was inside and immediately followed by a scream.


"Ojou-sama!" The bodyguard suddenly was beside her princess as she observed what the other girl was pointing at, and her eyes widened as she saw what was inside.


"Danzo-sama" One of the people in lab coats bowed to the old man behind the desk, the said man just nodded in acknowledgement.

"Status report on 009" The old man questioned as his gaze never left the person in a lab coat.

"Yondaime's seal is holding up well and the boy is slowly but surely integrating with Kyuubi's chakra."

"Excellent, finally the ultimate weapon is in Konoha's hand and with this we shall carve our names in the pages of history as the most powerful ninja village in the world!"


"How do you feel 009?" The voice held no emotion but the blond could make out the old war hawk's silhouette in the darkness.

"Nothing Danzo-sama." The blond gripped his short sword tighter as he looked at the body of his victim; the feeling of cutting down them down is invigorating the blond. The old man threw some washi to the blond, while the boy caught it with ease. 009 began wiping the blood off his short sword, as it seemed to glow in the light of the moon. The blond's eyes widened as he keeled over gripping his stomach as red chakra began seeping out of the boy. The old war hawk's eyes narrowed as he saw his weapon fall down, and with a quick chop to the back of the neck the blond was out like a light.

"It seems that there are still problems with the fox's chakra leaking." The old war hawk walked away as one of the members of ROOT carried the boy on his shoulders.


Parts of the cylindrical container began to move as smoke began to pour out of the tubes connected to the container, the two girls were slowly backing away from the object as the container door slid up. After the dust cleared the two girls went closer to the object, both of them were surprised to see a boy around their age with a mop of blond hair lying inside the container. The blond's eyes snapped opened revealing a glazed look that both girls noted.

"REGISTRATION NUMBER: 012607 OPERATIVE 009 ACTIVATION CONFIRMATION… NAME REGISTRATION…" The blond still lying in the containment unit stopped speaking as if waiting for something. Both girls looked at each other. The first one to speak was the small samurai girl.

"Konoka ojou-sama we need to go back to the main house."

"NAME REGISTRATION CONFIRMED…KONOKA…" The blond continued as Setsuna jumped infront of her princess. The blond boy stepped out of the container then went limp. The two girls went closer to the fallen blond, Konoka immediately checked the boy for any signs of life.

"Se-chan please call a healer."

"But ojou-sama…."

"Please Se-chan." The brown haired girl looked at the bodyguard with pleading eyes, Setsuna just sighed and shook her head and proceeded to run back to the main complex. The brown haired girl who stayed behind remained at the blond boy's side; she looked down at the fallen boy her hand slowly getting close to the blond's whiskered cheek.

"Ojou-sama." The young bodyguard came back with the elder healer and a house guard in tow. The elder healer turned the boy around and began examining the boy's body, the said woman gasped when she saw the marking on the boy's naval.

"Ren-san please carry the boy back to the main house." The guard nodded and carried the boy back to the main house as both girls and the elder healer back to the main compound.


The two girls, now behind the closed shoji door trying to listen in on the conversation between the Kansai Leader and the other elders.

"The seal on the boy's naval is the work of a master." One of the elders started.

"I agree but whatever the seal must be holding back is dangerous we must dispose of the boy as soon as possible." Both girls gasped as they heard the statement.

"No I will not tolerate killing children!"

"Then let us peak at the boy's mind to see what he is holding back, arrange the seals." The assistants nodded both girls are about to go then the shoji doors suddenly opened revealing the brown haired girl's father, Eishun Konoe. The Kansai leader just shook his head kneeled infront of the two girls.

"Konoka-chan, Setsuna-chan, what did I tell you about sneaking around?" Both girls looked to the ground embarrassed at being caught eavesdropping. The leader just sighed as he lead both girls inside the room with seals.

"Now both of you girls just stay close ok?" both nodded in response. The boy was placed in the center of the room and the seals were placed on different corners, one of the elders began chanting as the room began to fade and replaced by a cold sewer. One of the mages opened a door, his eyes widened at what he saw….


"009 here is your current assignment." The old man threw the file at the blond boy, to which the boy caught with ease. Quickly scanning the file then closed the folder after a minute of scanning the file, the boy gave the file back to the old war hawk then bowed.

"24 hours." The old man just smiled darkly as the boy vanished in the darkness.


The mage's eyes widened as he saw this and closed the door right away, the mage was breathing heavily after seeing the memory.

"What do you think the file is all about Eishun-sama?"

"I don't know let's keep on moving forward." The two girls clinging on his legs. Another door was opened then light flooded the room.


"Yo Ayame-chan, Teuchi-san." The old man with a pipe and a triangular hat walked in the ramen shop, with a small blond boy in tow. The old ramen chef just grinned at the incoming customer and motioned for them to sit at one of the empty tables.

"Ah Hokage-sama! and who is this young man?" The ramen chef kneeled infront of the boy lowering into eye level.

"This is Uzumaki, Naruto."

"Good good, now what will both of you be having?"

"I'll have two miso ramen." The chef nodded while calling to the back for Ayame to prepare the noodles while he prepares the broth. After a few minutes the chef came back, the boy at first just looked at the food infront of him. The kind old man gave him a small nudge forward, the boy slowly got some noodles on his chopsticks and slowly tasted the food served.

"How is it Naruto?" The boy just grinned at the Hokage.

"Looks like we'll be getting this little one as our number one customer." The Hokage and the Ramen Chef just laughed at the child's reaction.


The group just smiled at the boy's memory of the kind old man and the chef. Then the group just proceeded deeper into the tunnel and opened another door the room was enveloped in white light once again.


"Naruto…please live…live your life…" The kind old man coughed out blood as he shielded the blond, the boy just stared at the fallen Hokage with wide eyes.

"Kukukukuku how very valiant of you sensei." The pale man with snake-like features stepped forward.

"Jii-san…Jii-san…Jii-san…JII-SAN!" The boy was crying on top of the dead Hokage's body. The snakeman's features became clearer as he was once again holding the kusanagi sword.

"Now now it will be all over soon Naruto-kun." As the snakeman raised his sword to kill the blond , he stopped mid-swing as a suffocating aura came down of the battlefield that is Konoha.

"I'll kill you!" Everything went red.


The boy was now standing in the empty battlefield as the snakeman's body was lying down at his feet his hand was covered in blood, rain came down Konoha as if to wash its sins away. The boy heard footsteps coming from behind as the old war hawk stepped out of the shadows moving closer to the boy.

"Do you want power boy?"

"…." The boy continued to look to the sky as if looking for an answer on why the tragedy occurred.

"Throw away all these petty emotions and come with me, I will make you into the sharpest blade this world has ever seen." The man offered his hand to the boy. The boy looked at the old war hawk and slowly reached out to his hand. The war hawk just smiled darkly at his newly acquired weapon.


At the end of the dream Eishun was covering both Konoka and Setsuna's eyes from the scene of the battlefield as he was now breathing hard from seeing what the boy has encountered.

"Should we still continue Eishun-sama?"

"No that is enough I think its time we went back." With that Eishun looked at one of the elders who nodded then focused on canceling the spell, the man's eyes went wide as he felt something preventing him from canceling the spell.

"I can't cancel the spell."


"Daddy what's going on?" The brown haired girl asked her father remaining ignorant of the memory of the boy that just occurred.

"Were going to be fine Konoka-chan you do not have to worry about anything." Eishun kneeled infront of his daughter giving her and and her best friend/ bodyguard a reassuring look.

"It seems that whatever is holding us here wants us to see it , what should we do Eishun-sama?" The leader stood up and examined his surroundings before giving the other man an answer.

"Then we have no choice but to press forward." One of the mages opened the door and for one last time the room was covered in white light.


"Mizuki you are under arrest for treason." The blond boy just looked at the silver haired chuunin with cold eyes.

"Heh gaki coming alone is your biggest mistake." The Silver haired chuunin whistled, 20 Iwa shinobi came out of the shadows surrounding the boy. 009 merely put a finger over his ear covering the earpiece and started talking on the small mike piece on his collar.

"Requesting permission to eliminate the traitor and 20 Iwa shinobi." one of the Iwa shinobi began attacking, the blond dodged the attack by backflipping over the man and as he was in the air the line responded.

"Permission Granted." The boy grabbed the Iwa shinobi that attacked then twisted the man's head, the sickening crack resounded through out the forest and the man fell down dead as the boy landed gracefully to the ground. The other iwa shinobi became hesitant to attack as the boy once again looked at them with cold eyes, then drawing the kodachi from scabbard strapped on his waist. Mizuki was now sweating as he saw the boy take out one of this Iwa shinobi without batting an eye, then steeling his resolve to take out the demon container the drew the large shrunken from his back and threw it at the boy with blinding speeds. The blond boy saw this and grabbed the large shrunken mid-air and redirected it back to the thrower hitting Mizuki in the head, the said chuunin dropped like a log.

"Shit! Kill the bastard!" The apparent leader of the iwa shinobi ordered the others to attack the boy, some of the iwa shinobi began making hand seals and launching earth spires at the boy to which he just vanished and reappeared beside one of the shinobi then swinging his kodachi effectively beheading the nin. Another Iwa shinobi tried to cut the boy in half with a rather large sword, 009 just parried the blow and drove the kodachi under the man's chin effectively killing him, he placed another hand on the handle of the kodachi and pulled it out though the man's face cutting it in half. blood splatter on the boy's face as he ran towards another nin while dodging multiple jutsus being thrown at him, then jumping to dodge the sword swing coming at him all the while stabbing the attacker in the neck with bloodied kodachi. The boy started to do hand seals and as he finished with the hand seals he promptly vanished as an earth spire popped out from the ground.

"Katon: Gokakyu no jutsu." The blond released a large fireball at point blank range instantly incinerating 4 iwa shinobi. The remaining iwa shinobi began to retreat, the blond did a tiger seal and created several shadow clones, said clones nodded to each other and proceeded to systematically eliminate the retreating shinobi. The boy was closing in on the last shinobi as the he was shaking in fear holding up a kunai.

"Don't hate me for this, hate whoever told you to assist the traitor." The boy promptly ended the remaining shinobi's life.


"Dear Kami, this boy was an assassin!" One of the elders exclaimed. Eishun removed his hand once more from both girl's eyes once more preventing them from seeing the fight though Setsuna managed to see bits and pieces of it and was unsettled how easily the boy can kill. After passing though the last door the group managed to reach the a large hall and at the other side a gate with a piece of paper with the fuuin symbol was written. An ominous presence came down upon the group, Konoka passed out from the presence her bodyguard though in one knee managed to stay beside her charge. A large slitted eye became visible to the group as multiple torches lit up from different sides of the wall.

"WORTHLESS FLESHBAGS, I SHOULD DESTROY YOU RIGHT NOW!" The group was terrified that from behind the cage a large nine-tailed fox staring down at them and thrashing around his prison.

"That is enough Kyuubi!" The group looked towards the source of the voice, stepping out of the shadows was a young boy with blond hair and blue eyes. The boy and kyuubi have a glaring match before the fox begrudgingly retreated back to its cage.

"I'll always be waiting for an opening you hairless ape and when that time comes…" The boy just stared at the retreating form of the fox before looking at the group, the boy suddenly bowed and vanished into the shadows. The people in the room noticed that the room was going back to normal as they saw the body of the boy in the middle of the room was becoming visible once again. Konoka began to stir from her passed out state and smiled as she saw she was lying in Setsuna's lap.

"What do we do now Eishun-sama?" asked one of the elders. Eishun eyed the boy critically, something was telling him that the boy was a vital component that would shape the world of magic forever.

"I'll take care of him." Eishun responded and with that the boy known as 009 was in the care of Eishun, Konoe.

"What do we call him?" Eishun remembered the kind old man from the boy's memories.

"Naruto, we'll call him Naruto."

After the night's events Naruto was taken in by the Konoe family and raised as Konoka and Setsuna's older brother, though very silent he always accompanied the two wherever they go. The two girls began growing close to the blond despite his lack of emotions, to the girls he was the perfect onii-chan. Naruto would spar with Setsuna all the while giving her some tips about fighting while Konoka watched the two with a smile and Setsuna was intently listening to her brother's few but wise words.


"Onii-chan, Se-chan, look look." Konoka(wearing a white kimono with a pink obi) was running excitedly around the festival grounds while both Setsuna(wearing a blue kimono) and Naruto (wearing a black yukata) followed the hyper active girl.

"Ojou-sama, matte!" The young bodyguard picked up the pace as she followed the other girl while the older boy continued walking at a relaxed pace. The older boy suddenly stopped when he saw something in one of the shops, the boy entered while both girls were running around. After a few minutes the boy came out once more with a small bag then proceeded to locate the two girls, and after a few moments of searching finally found the two.

"Konoka, Setsuna." Both girls looked over to the source of the voice and smiled as their big brother gestured for them to come over. As both girls reached the older boy, he began leading them towards the main shrine.

"Onii-chan, where are we going?" Naruto just pointed at the shrine, both girls just nodded and quietly followed the older boy. Upon arriving at the shrine the older boy kneeled infront of the two girls and took out two pieces of jewelry out of the bag. The girls eyes' widened as they saw the two cross pendants, one was has a blue jewel at the center while the other one has a red jewel at the center. Naruto slipped the chain with the pendant with the blue jewel around Konoka's neck and once the boy was done he began slipping the red version of the same pendant around Setsuna's neck while Konoka was looking at the jewelry with a small blush. Once Naruto was done he looked at both girls and smiled which made both girls blush more.

"I'm glad that it looks good on both of you, and with this we'll always be together no matter where we are." He took out earrings that look like minature versions of the pendant (one was red while the other was blue) and clipped it on his ear. Konoka gushed how cool he looked while Setsuna has a look of admiration as she looked at the older boy. Then both girls were surprised when he did the unthinkable, their onii-chan smiled for the first time. Both girls were blushing at how he looked when he smiled. Konoka was getting more and more giddy inside as she suddenly jumped into Naruto's arms and hugged the older boy, Setsuna did the same thing only a little more reserved.

"I'm going to marry onii-chan when I grow up!" Naruto just tilted his head to the side while Setsuna was blushing and stuttering all around.

"B..b..b..b..b..b..b..but o..o..o..o..o..ojou-sama thats…." The swordsman looked away while Konoka was grinning at her.

"Ara Se-chan I thought you love onii-chan too?" While the exchange was going on Naruto could only look at both girls with question marks floating above his head, Setsuna stopped moving for a few moments then promptly passed out as she finished processing Konoka's words.


A man in a ninja mask was running down the streets with a brown haired girl limp in his arms.

"Heh now it seems that we have the Kansai Magic Association's attention with this girl as hostage." The man continued running but stopped as he saw a figure on the other end of the street. The man eyed the figure carefully then grinned as he saw who the figure is. The boy stepped forward out of the shadows and revealed himself to the man. Naruto was now wearing a black hakama and a short sleeved gi with a kodachi strapped on his waist , the man waisted no time summoning his allies to battle as multiple shinobi came out of the shadows. The boy had a sense of deja vu in his current situation, the boy spotted Setsuna coming from the opposite direction. One of the nins jumped towards the blond attacking him, Naruto simply leaned to the right and drew the wakizashi taking the man out of the fight. The man carrying Konoka saw this and finally realized who the boy is.

"Don't move or she dies!" The man held a kunai at Konoka's throat. Setsuna and Naruto gritted their teeth as the man backed off, distracted one of the nins threw a kunai at Setsuna hitting her in the shoulder. The young bodyguard cried out in pain as the weapon pierced her flesh.

"Se-chan! Onii-chan!" Konoka called out to both as she was trying to struggle against the nin. The nin carrying her punched the girl the in stomach making the smaller girl gasp for air and falling limp in the man's arms.

"Stupid brat!" Setsuna's eyes widened at the man's brutality as she herself was attacked by the nin and then…

"Setsuna!" Naruto's eyes widened as he saw Setsuna stabbed in the back by the nin. As the man was standing up a great weight fell upon the area as most men got down in one knee and suddenly finding it harder to breathe, the enemy nins were looking for the source of the raw killing intent and all eyes fell to the boy as he began emitting red energy, then raising his head revealing red slitted eyes. The nins began running and the one carrying Konoka promptly dropped the girl trying to escape.

"There will be no escape." The boy said with no emotion and suddenly vanish appearing on the path of the escaping nins preventing their escape. The boy raised his hand and the surrounding red energy took the shape of a large claw and grabbed the man's head, said victim was screaming in agony as he felt his skin being burnt by the malicious red energy. Konoka woke up and her eyes widened as she saw Setsuna's body on the ground, she stood up and frantically ran towards the other girl's body ignoring the nins running past her. Once she reached the girl's body she quickly covered the wound on the girl's back and she began crying while trying to cover the girl's wound.

"SE-CHAN PLEASE DON'T LEAVE ME!" And as if her prayers were answered the other girl's body began to glow as the wound on her back began to close not even leaving a scar. The other girl began to stir awake and she rolled around to see her best friend crying over her.

"Kono-chan…"Konoka's eyes snapped open as she saw Setsuna free from injuries, and promptly hugged her friend. Both girls were crying as they were hugging as if to confirm the other's existence but a shout snapped both girls out of their thoughts.

"Please spare me!" Both girls saw the younger boy covered in blood with the red aura surrounding him in the form of a fox with a single tail, his hand around the other nin's throat as he was glaring at the man with slitted eyes.

"Don't hate me for this, hate whoever gave you your order. " And with a squish the man's neck snapped with an audible crack. Setsuna's eyes widened at the blond's words and began to shook as she remembered Naruto's memories. Rain began pouring at the scene as if the heavens trying to clear the field of blood, the blond continued to stare at the sky. Both girls were slowly stood up at the blood covered form of their brother. Konoka was the one who spoke first.

"Onii-chan?" The brown haired girl slowly began to make her way to the older boy, the blond did not move and continued to stare at the sky his normally spiky blond hair was now down due to the rain.

"Onii-sama?" Setsuna followed the brown haired girl going towards the older boy.

"DON'T!" Both girls stopped surprised at their brother's words, it pained Konoka and Setsuna to see their brother in this state.

"Please don't come any closer…" The blond pleaded while still staring at the sky his eyes now being covered by his wet hair.

"Setsuna promise me you will never leave Konoka's side."


"Please Setsuna…" The older boy finally looked at both girls and they were surprised to see the normal blue eyes was now slitted red.

"Hai onii-sama I will guard her with my life."

"Thank you…" The older boy began to walk away from the two girls.

"Onii-chan, where are you going?" The brown haired girl asked, the blond momentarily stopped…

"This is something I have to do, gomen ne Konoka, Setsuna…"

"No….. Onii-chan please…. don't leave…." Setsuna lowered her head to prevent anyone from seeing tears as the older boy left. Konoka started crying as she continued to call out to the older blond but he continued to walk towards the darkness.

"Onii-chan…Onii-chan… ONII-CHAN!"


Setsuna woke up panting as she gripped her chest then looked at the red pendant hanging on her desk, the girl glanced at the clock reading "4:30 AM". The black haired girl stood up and began to change into her training gi and hakama, she got her sword and finally came infront of the red pendant before grabbing it and sliding it around her neck and ran outside the dormitories towards the clear field nearby.

'Its been a while since I had a dream about onii-sama, Kono-chan's memories has been modified to forget any memories of you but she knows something is missing…Onii-sama where are you?' the girl took another swing in the air. The shadow sword fighting continued for 3 more hours at the end of the training she began panting as she finished the last swing. Looking at the clocktower nearby she went back to her dorm room and changed into her school uniform and made her way towards Konoka's dorm room. As she neared the room the shouts of indignation began as she heard Asuna shouting while Negi was frantically apologizing for going into her bed again. Konoka heard the knock on the door.

"Ara Se-chan come in, come in." She ushered the other girl into the apartment, as Setsuna entered the room she giggled at the sight of Negi sitting in a seiza position while Asuna was screaming at the younger boy.

"How many times do I have to tell you not to get into my bed!"

"B…b…b…but Asuna-san." The child teacher was now in tears. Setsuna caught both their attention with a cough, when both of them looked at the other girl, she merely pointed at the clock, Asuna's eyes widened as she saw the time and began mumbling about how she hated brats.

"Arigatou Setsuna-san." The child teaching was bowing comedically infront of Setsuna.

"Negi-sensei, isn't there a meeting your suppose to be going to?"

"AHHHHH! Gomen ne Setsuna-san, Konoka-san I need to go." The child teacher ran out of the room as Setsuna sighed while Konoka was just giggling at the scene.


Negi was now running down the road as he tried to get to the teachers meeting on time, though due to his haste he slammed into a taller man. The man just turned around and looked at the fallen child teacher.

"Itai…. Gomen ne I am in a hurry…." The man offered him a hand, to help him get up. The child teacher stopped and examined the taller man.

"Its not a problem… Negi-sensei, I have to go." The blond man began walking away.

"How did he…." The teacher blinked in confusion at how the blond man knew his name.


"Asuna-chan we need to hurry were going to be late!" The three girls sped down the pathway going to the pathway littered with sakura trees. As they were running down the path Konoka noticed Setsuna slowdown as she stared at someone in the distance.

"Onii-sama?" Konoka's eyes widened as she heard this and followed Setsuna's line of sight, tears began to form on Konoka's eyes as she began to remember the memories that was sealed years ago. Asuna stopped running as she saw her friends reaction to the guy standing near the sakura tree.

"Onii…chan…" Konoka mouthed, the man turned around and observed both girls.

"Konoka, Setsuna…" The two continued to stare at the man as sakura petals danced around the area.