Canon until the events begin in the Forest of Death.
Orochimaru slammed his five point seal into Naruto's stomach. The blonde boy screamed in pain and passed out. The Snake Sannin let the limp form of Naruto fall towards the ground but Sakura managed to catch and pin his jacket to a tree with a well thrown kunai.
The jacket lifted up to reveal the seal on is stomach. The black ink of the seal began to pulse red in time to the boy's heartbeat as the extra five point seal played havoc with the chakra of the Kyuubi within Naruto's body.
Within Naruto's mind and soul, the cage of the Kyuubi flickered as the seal was beginning to fail. The residual energy the Yondaime Hokage had left in the seal as a safeguard materialized and looked at the demon the seal held.
"Your power will not be released today, kitsune," the Yondaime said as he pushed his remaining chakra into undoing the damage the five point seal had done to his and his wife's ultimate creation in the sealing arts.
The Kyuubi no Yoko grinned as much as his form would allow as the Death Reaper Seal failed beneath the full power of its unrestrained might.
"You cannot stop me human. The interference of the additional seal has forced this one open," the Kyuubi no Yoko shouted in glee as his spirit passed through the now opened bars.
The Yondaime shadow clone knew his power was rapidly depleting but finished destroying the five point seal on his son. The bars of the cage began closing quickly as the Kyuubi was not completely out of the cage.
"I might not be able to stop you completely, but your victory shall be a hollow one, demon. I'm sorry Naruto," the Yondaime said as he sped through dozens of hand signs in a different and forbidden jutsu.
"Flesh Clone Technique!" the Yondaime roared as the Kyuubi no Yoko was nearly through the cage door. The bars solidified once more cutting off the tails of the demon fox and leaving them within the cage.
"My power!" the tailless fox roared as it found its consciousness being pulled out of Naruto's mindscape.
In the forest, red and blue energy began to swirl about the pinned form of Naruto. Orochimaru and Sakura looked on in horror as the energy formed a sphere around the blonde boy
'You think you have won but I have a trick of my own, human,' the Kyuubi no Yoko thought as it manipulated its own energy within Naruto's body as the flesh of Uzumaki Naruto was torn asunder.
Sakura could only stand in awe as the multicolored sphere began to stretch out; first into an ovate shape then pulling in opposite directions. The red chakra swirled around one side and the blue chakra around the other until two separate spheres of swirling chakra hung in midair. The light faded until two forms appeared within them only to fall to the ground below as the chakra faded.
'This is very interesting,' Orochimaru thought. His plan to mark the Uchiha boy could wait. If the demon escaped, he would be killed as well and his life was more important than his next vessel. If this was something else entirely, his patience would bring him something new that even he had only heard rumors about. True immortality might be within his grasp. The Snake Sannin turned and headed out of the Forest of Death while avoiding the approaching ANBU and test proctors, including his own former apprentice.
The kunoichi of Team 7 jumped to the ground to see if she could help either person but was shocked at what she saw. A frail looking Naruto and a girl with the same hair color and a fading black seal on her stomach lay unconscious in the dirt of the forest. Both looked extremely emaciated and both were barely breathing.
Sasuke dropped down to the forest floor more out of curiosity than a desire to help. He pushed his hands into his pockets as the first outsiders arrived in the area. Several ANBU and the proctor Mitarishi Anko had weapons drawn and were looking for a fight until the squad captain gave an order to stand down.
The people all stared at the pair of blondes on the ground. Neither one looked like they would be awakening at any time soon. The squad captain spoke, "Who witnessed this?" he asked.
Sakura slowly raised her hand and said, "I did."
The man in the mask nodded and point to both blondes and Sakura. "Mitarishi-san, please bring the Uchiha back with you. Deliver him to the secure wing of the hospital."
Anko nodded but Sasuke protested.
"We're in the middle of the Chunin Exam here, we can't just leave!" he said until a quartet of masked faces looked at him. The combined killer intent nearly matched that of the woman he had just faced so the boy quickly quieted down.
The blondes were picked up in the arms of a pair of ANBU who vanished with the captain in a swirl of leaves by shun-shin jutsu. The last remaining ANBU gestured to Sakura who stood up. He took hold of the girl's arm and vanished. Anko just grabbed Sasuke by the collar and vanished as well.
Some time later in the hospital, the Sandaime Hokage, Sarutobi Hiruzen looked into a room lined heavily with security seals. The male blonde lay in the room with several intravenous lines running into his arms. Nutrients and fluids ran down the lines and into his body. Residual traces of the original jutsu were pulling the infusions into the body as fast as they could be administered. The aged man knew that the girl in the next room was receiving the same treatment. The leader looked to the medic in charge.
"What do you have to report?" the leader asked in a low voice.
"Both subjects are processing whatever IV fluids and nutrients are given to them at an astonishing rate. Our specialists cannot identify the jutsu used to create this but both subjects are human. Sir, initial tests show the boy matches Uzumaki Naruto's genetic structure exactly but the girl poses a problem. Without a specialist we can only guess but the girl seems to partially match the boy, as if a twin but preliminary tests show a difference."
"Explain," Sarutobi said in his quiet voice.
"It is not easy to explain, Sir," the medic hesitated. "You understand how the genes for gender work correct? Males have an XY chromosome pair and females have a XX chromosome pair. The boy as I said matches Uzumaki Naruto's pattern exactly but the girl does not. However, the X chromosome in the girl matches that of Uzumaki Naruto and her two X chromosomes appear identical to one another. That may cause problems later on but for now it is not an issue as she seems healthy. We are going to have to to a detailed analysis of the other genes to see what else has changed.
Sarutobi nodded slowly. He understood the basics but they had few doctors or medics who dealt with genetics at that level. The village was good at some aspects of genetics but frowned on direct manipulation in any fashion. The Hyuuga routinely screened clan members for bad recessives before allowing children to be conceived but that was the limit of what was done in Konoha.
To make matters worse, the one person who was most knowledgeable in genetics was Senju Tsunade. She was nowhere near the village and refused to return. Sarutobi grumbled and decided that he had enough of that. The boy he loved as a grandson was in a bad way and his student was going to have to face up to her past one way or another.
Sarutobi walked to an unoccupied room nearby and made some hand signs. He pressed his hand to the floor and said, "Summoning Technique." The chakra smoke cleared to show an eight foot tall monkey with a Konoha headband on his forehead.
"Enma, I need a favor from you," Sarutobi began before the Monkey Lord could speak. "I need to know if your people have contact with the Slugs that Tsunade summons."
"That is an odd request, Hiruzen, but we can contact them. Why?" Enma asked in his deep voice.
"I need the slugs to bring Tsunade back here at once. They can reverse summon her to their realm then re-summon her here. I do not want to spend weeks or months searching for my student and I need her expertise right away," Sarutobi explained.
Enma nodded. "I understand and approve. I will make the request of them. It may take a few hours as intermediaries are required. If you have a physical message I can present to the slugs it will make things easier to arrange."
"Give me an hour and I will have a lesser monkey bring it you, my friend," Sarutoib said.
Enma nodded and vanished in a puff of chakra smoke.
Tsunade was nervous. She had hit several jackpots in a row. She had enough in winnings to pay off her debts plus interest. Her apprentice Shizune stood by as the Slug Sannin moved to another machine and fed money into it. The wheels spun and came up on the jackpot once more. Tsunade paled as the money poured out and a floor boss was forced to count out another jackpot.
No sooner had she passed the winnings to Shizune when a small slug approached the group.
"Tsunade-sama, it is imperative that you come with me. A situation has arisen that in Konoha that needs your personal attention," the slug said in a soft voice.
Tsunade had been expecting something bad to happen and now she understood her winning streak.
"I am not going back there," Tsunade growled to the small blue and white slug.
"Forgive me, Tsunade-sama but you leave us with no choice," the slug's voice said in a sad tone.
The slug plopped down on Tsunade's foot and both the blonde woman and the slug vanished in a puff of smoke.
Shizune looked on in awe and then looked down at the money in her hands. She hurried back to her room to get the luggage and Tonton before she could head home for the first time in over a decade. A visit to various money lenders along the way was also planned.
Tsunade was cursing louder and fouler than any time in Sarutobi's recollection when she appeared in his office. The slug that had been waiting there dispersed itself.
The blonde woman glared at her former teacher. "What the hell are you thinking doing this to me Sensei?" she shouted.
Sarutobi let the woman yell for another few seconds before he stood and glared back while releasing a killer intent that would have given Orochimaru pause. Tsunade stopped and backed up a step in shock.
"That is enough out of you, Tsunade," the Hokage spoke in a low voice. "I called you back because I needed you here for something of great importance. If I had the time to waste I would have recalled you through normal means but time is of the essence."
The Hokage held out a medical folder to the legendary medic. Still stunned quiet by her teacher's show of will, she took it and opened the folder. She scanned the first page and then sat in the chair behind her to flip through page after page of information while muttering the whole time, "This is impossible."
"If it is impossible, Tsunade, then you should tell it to the two people lying under heavy guard in the hospital security ward," Sarutobi replied.
Tsunade came out of the room and pulled off her gloves. She had made a thorough exam of both tweens and was shocked by what she had found. Both still had not awakened but more information meant more confusion.
The boy seemed to be completely normal in every respect except one. All of his skin was new and unscarred while the girl had fine scarring on her from training injuries. The boy had no seal on his stomach while the girl does. The boy was in every possible test Uzumaki Naruto while the girl was showing signs of not being him. Her eyes had shifted color to more of a purple and the roots of her hair were coming in red instead of the blonde that was showing. The Sannin had also performed an inspection and found a complete female reproductive system in the girl although not yet active. A slight hint of breast development was starting to show as the girl gained weight from the intravenous feeding.
Sarutobi looked at Tsunade.
"Well?" he asked.
"Congratulations, Sensei, its twins," Tsunade remarked sardonically. "Judging by the end result and the witness testimony of this Sakura girl, I would guess some kind of flesh clone jutsu gone wrong."
"Flesh clone? Is that even possible?" the older man replied in shock.
"Possible, oh yes. I had seen the incomplete jutsu scroll for one a long time ago when the creator had some medical questions. It takes a lot of chakra and a lot of body mass to accomplish. Well body mass or a vat of something to make the new body from. It was created by one Uzumaki Kushina from the forbidden sealing scrolls of Uzushio. She never got past the concept phase."
"As you know, she had been from the Land of Whirlpool and the previous jinchuuriki for the Kyuubi. She came up with the idea in a moment of anger over her situation. Her original intent had been to split herself in two with the Kyuubi's essence in the flesh clone and be able to kill it since it would have no power of its own. But she never used it," Tsunade finished.
"What stopped her from doing that?" Sarutobi asked.
"The Yondaime forbid it and then she found out she was pregnant with the blonde gaki over there," Tsunade replied while pointing to the room holding the boy.
Sarutobi looked at the girl still unconscious behind the glass. "So what would go wrong with one not being a clone of the other?"
"That part I couldn't tell you Sensei," Tsunade said. "I couldn't even tell you which one is which right now. The girl shows signs of being the original and the boy being the clone but how did one become a girl? There are too many unanswered questions. Are both Naruto? Is one Naruto and one the other the Kyuubi? Heck, are both even going to wake up would be the next question. There is so much we are unable to even guess at right now."
"What I can tell you is that the jutsu used what mass Naruto had and split it between the original and the clone. That is why both are so badly thin and drained right now. Their bodies are trying to rebuild the flesh and complete the jutsu which is why traces of the technique are still detectable. It should dissipate as the subject's weight reaches original levels. After that, I would burn every record we have gotten so far on this technique or put it in a black file before someone who shouldn't get a hold of it."
"But for right now, I need to do two things. First is I need some sleep and to wait for Shizune to get here from Tea Country. The second …"
Tsunade spun and punched Sarutobi in the face hard enough to break his nose and send the old man back into the wall behind him.
"That is for messing with me and dragging me back here, Sensei"
Days passed in the hospital while events unfolded within Konoha. Five teams passed the second test of the Chunin Exams and advanced to the Finals without an elimination round; a team from Suna with the Kazekage's children in it, a team from Rain, Team 10, Team 8 and Team Guy.
In the hospital ward, Tsunade kept a watch on the pair of children. The intravenous feeding had gone on for a week until all signs of the jutsu had faded from both the boy and girl and both appeared normal to all medical scans. The blonde boy looked exactly as Naruto had when his team was asked to identify him.
The girl was a different matter. Her initial whisker marks had faded to mere white lines on her face but would be noticeable if she tanned heavily. Her irises had become fully purple and her hair was coming in a red few remembered seeing. Her face softened and took on a different cast but was still recognizable as Naruto. Even her body changed as she gained weight she developed the modest but noticeable breasts and hips of a girl about twelve to thirteen years old. Tsunade shuddered when she recognized the overall look as that of her distant cousin and Naruto's mother, Kushina.
'Of course, it should. With only the maternal DNA to work with, only the attributes of Kushina and none of Minato's would be there to build with. This could become a huge problem later on since Kushina was quite a beauty.'
A buzzing noise from the boy's room alerted the medics to a change. A nurse went in to see the boy first. Tsunade waited for the Hokage and ANBU to arrive before going in to see what would happen.
The blonde boy was practically bouncing off the bed. She wondered how anyone could be so hyper after just waking up after all he had been through.
"Hey, Old Man, why am I in here?" the boy yelled out as soon as the Hokage had entered the room.
The Hokage smiled gently at the boy. "You have been very sick. You only just woke up and we need to make sure of a few things. Now, this doctor has been taking care of you and never met you before. Could you introduce yourself to her?"
"My name is Uzumaki Naruto and I am going to be Hokage someday! Believe it!" the blonde boy crowed out with his bright blue eyes seeming to shine with confidence.
Tsunade arched an eyebrow at the boy then looked at Sarutobi. "You sure he is not brain damaged, Sensei?" she asked.
Sarutobi chuckled. "No, that is normal for him," he replied.
A high pitched cream from the other room alerted them to the girl waking up.
The Hokage and Tsunade hurried to the other room to see the girl with a panicked look and clutching her chest muttering "Dispel. Dispel. Dispel!" She looked up as the people entered the room.
"Old Man! Why do I have boobs? I must have done my Sexy Jutsu somehow but it won't go away!" The girl was crying in her panic by this point.
"It's going to be all right. Could you tell me your name?" Tsunade asked the girl.
"My name is Uzumaki Naruto," the girl replied.
"Well, this certainly is a situation," Sarutobi said as he headed up to his office. It had taken almost an hour for the girl Naruto to calm down. Even then Tsunade felt she should be monitored at all times and Sarutobi assigned an ANBU guard to stand watch in each room now that the children were awake.
Sarutobi hoped that Ibiki could learn something from them in his 'informal chats'.
Morino Ibiki was not afraid of many things. He could count on one hand the things that even bothered him to any extent. Clowns, disease, incapacity of his mind; those things were on the short list that he was aware of until this point. Meeting the girl in this situation would forever be added to his list.
It had begun well enough. He turned on the recorder and sat back.
"For the record, I need your name, age, and team," Ibiki asked.
"You're that scary examiner guy, aren't you?" Naruto asked.
Ibiki nodded. "The sooner you answer my questions, the less scary I will be."
"Um, Uzumaki Naruto, age 12, and I am on Team 7," she replied.
"Good, now, tell me about the events in the Forest of Death."
"Well, I got blown away from my team and this giant snake ate me. But I blew it apart by using my Shadow Clone technique and escaped. Then I hurried back to my team only to find some scary Grass lady threatening the teme and trying to get our scroll. I saved him and then the lady gets mad and brings out another huge snake and it attacks the teme but I save him again and called him a scaredy cat. Then I get um a bit wild and attacked the Grass lady. I start beating her but then she pulls out some jutsu and I ended up in here like this. The doctor Tsunade said they were looking into seeing what caused it and I shouldn't worry yet."
Ibiki arched an eyebrow. 'I don't think she even took more than one breath during that entire statement.'
"Is there anything else you recall while you were out? A dream perhaps?" Ibiki asked.
Naruto thought for a moment. "All I can remember about dreams is someone saying 'I'm sorry, Naruto' but I don't remember seeing anyone," she said after a minute.
Ibiki nodded and switched to more mundane questions that he could verify by asking Naruto's teammates and teacher.
As he got up to leave, the girl asked him a question.
"Ibiki-san, will they be able to make me a guy again?" Naruto asked.
Ibiki was taken by surprise by that. He knew he should not give out anything but the tone of a scared girl got to him.
"I am sure they will be able to get things the way they should be, Uzumaki," he said after a moment.
Ibiki walked out and headed to the boy's room. He was bothered by the thought of losing everything that made him who he was and waking up powerless to do anything about it. It immediately went to number two on his list; right below clowns.
"Both children gave near identical stories Hokage-sama," Ibiki reported. "While a few words were different the details are the same. The background questions and answers match as well. My routine doubling back and cross examinations of both yielded no discrepancies. They both answered the identity verification questions in the files correctly. If one is lying then without some intense interrogation techniques, I would have to say in my professional opinion that BOTH are Uzumaki Naruto."
Ibiki got up and left after that. The Hokage looked at Tsunade and then to the recently arrived Jiraiya, his final student. "So, any ideas?" he asked.
Tsunade spoke first. "I am about out of tests I can run on them. Neither one is showing any signs of deterioration or instability. The girl is already showing signs of the Kyuubi chakra beginning to leak from the seal but according to existing reports, that is a designed allowance. Her body is actually converting it to normal chakra faster than previous tests show. She is going to be a powerhouse when she gets her strength back."
"The boy is another issue entirely. His chakra levels are jonin level already, Sensei. He might not be at full capacity yet either. However, he is showing no signs of anything that is not human about him. He could literally be what Naruto might have been if he had never been inflicted with the Kyuubi. He is what the son of the Fourth could possibly have been like," Tsunade finished.
Sarutobi nodded. "That is a problem for us. We cannot do anything to the boy because he looks like Naruto and is completely normal otherwise. We cannot do anything to the girl because she has the Yondaime's seal on her. Without more conclusive evidence, we do not know which is which. People are asking questions. We have kept all of Team 7 in isolation up until now but we cannot hold them forever."
A knock on the door interrupted Sarutobi.
"I am sorry to bother you. We have a situation down in the secure ward with the girl," the nurse said in a winded voice.
"What's wrong?" Tsunade asked.
The nurse looked at the Hokage then at Jiraiya before looking back to Tsunade. "She tried to use the bathroom and now is in there crying and won't come out."
Tsunade gently knocked on the bathroom door. "Naruto, open up," she said in a gentle voice.
"It's gone," whimpered a voice from the other side. "How can they fix me if it's gone?"
Tsunade closed her eyes and pinched the bridge of her nose. Of course that was the problem. "Naruto, you need to open the door and come out or I will break it down. We can fix this," she said in a less gentle voice.
"Can't be fixed," was the only reply followed by more sobs.
"Naruto, are you leaning on the door?" Tsunade asked.
"No, leave me alone," the girl replied.
Tsunade smirked and punched her hand through the door next to the knob. She then reached over and unlocked the door before opening it. The girl looked at her in shock with wide eyes as Tsunade stepped into the small room.
"Okay, time for lesson number one. Female equipment and how to use the bathroom," Tsunade said as she stuffed a towel into the hole in the door and closed it behind her.
The male Naruto had heard the commotion nearby but pretended to ignore it. The sclera of his eyes flashed red for a moment before returning to the normal white.
'Remember, playing the fool is your safest plan right now. Keep your true self hidden Naruto. As far as they know or can prove, you are the true Naruto. In due time, we will get what is ours,' crooned the voice in the back of his mind.
The boy kept himself from nodding. He was free from that smiling moron at last and he planned to stay that way. He had no idea how or why this had happened but he would make the most of it. When the time was right, vengeance on those who had ignored or tormented him would be sweet indeed.
Deep within the boy's mind, a second presence was hiding.
'Separating the real Naruto from that grinning fool and damaging the original body enough to cause the jutsu to rebuilt it as a female took most of my remaining power. I will regain the power but it will take time. I am vulnerable now in a way not known since the time of the Six Path Sage. My continued existence depends on this boy until I can gather enough chakra to reform a body of my own. Once that happens, I shall recover my power from behind that blasted seal and leave this place a ruin. Then to find the Death god, recover the rest of it and devour the soul of the man who dared stand up to me.'
Next Chapter: Separate Lives
Flesh Clone Technique (File Mention only: Further research on this of similar jutsu forbidden)
Created by Uzumaki Kushina
Rank: A (Yondaime Hokage Note: Beyond S)
Hand Seal Sequence: Initial test: 87 seals (Sequence Deleted by Yondaime Hokage)
Jutsu Notes: The jutsu intends to create a duplicate body of a person out of the flesh or substitute material available. Intellect would be limited but uncertain as to how much as the jutsu has never had a practical test. Initial test of jutsu performed on a lab animal resulted in identical animals being created. Further animal testing recommended before use on human subjects considered.
Forbidden: Any further use or researching of the jutsu is banned by Yondaime Hokage and all other records and notes pertaining to the jutsu destroyed.
This story is a plot idea that had been in my head and flash drive for some time. It uses the initial plot concept pioneered by EroSlackerMicha in his story 'He Said, She Said' with a major difference. Instead of Naruto merely becoming a girl, he is instead split into two beings. The original body was intentionally damaged by the Kyuubi by destroying the genes the Yondaime provided and the jutsu rebuilt the body as female using the remaining chromosomes. The flesh clone contains the Evil or Yami Naruto seen briefly in recent manga. My original concept had only the Kyuubi with a copy of Naruto's memories but using the new idea from Kishimoto may only add to the tension as both are in fact Naruto. Artistic license allows the jutsu to work as stated by me since I created it.
Please note, updates on this story will be slow in coming
Edit 12/14/10: Fixed vague references to only the Y chromosome being destroyed. The intent as written was for all of the Yondaime's genes to be deleted