Summary:

What if Naruto was a girl all his life? What if she was experimented on and imbued with the Shodaime Hokage and Uchiha Madara's DNA after EMS and rinnegan? What if she had her mother's bloodline?

Two young people were standing on two large opposing statues near a waterfall. The blonde, known as Konoha's most unpredictable ninja, was screaming at her team mate. The raven haired boy wonder stared impassively ate him and just got into a battle ready stance. The two leapt at each other and the ping of metal against metal was heard. They both landed on the water and the blonde rushed the other with a tearful scream. He was kicked back and fell under the water's surface. Uzumaki Naruto thought about everything that had happened and made a promise to himself. He pulled himself onto the water's surface and faced Uchiha Sasuke.

"Sasuke! I will bring you back, even if I have to break every bone in your body." Naruto shouted.

"Naruto, you are too weak. You would not understand my pain. My hate is what makes me strong enough to kill my brother. I will achieve my ambition even if I have to surrender my body to Orochimaru." Then suddenly Sasuke's eyes changed. A third tomoe shifted into each of his eyes. His sharingan was finally complete. He put his headband on and charged Naruto. He was winning until red chakra enveloped Naruto's body. He activated the curse seal but level one was not enough. The chakra around Naruto morphed to form a silhouette of a fox. Sasuke changed into a purple creature resembling a hawk with large hands for wings.

Naruto charged up a rasengan and Sasuke retaliated in this show of power buy preparing his chidori. Sasuke flapped his wings and was airborn while Naruto, filled with a portion of kyuubi's chakra, launched himself at him. The two attacks collided and they formed a sphere of condensed chakra, disrupting the flow of water from the waterfall.

When the attack ended, it began to rain. Naruto was on the other side unconscious. Sasuke dragged his feet to Naruto and felt the aftershock of pain from Naruto's attack and knelt near his forehead, looking down at him.

To his surprise, Naruto's features began to change and became slighter. His hair grew out until it surrounded his head until it looked like a messy and rater large crown. It still retained its golden sheen. The face became more feminine and two bumps could be seen through the soaked orange tracksuit top Naruto always wore. The body's proportions changed and made the legs longer.

Realizing he had spent a lot of gawking he ran up and over Uchiha Madara's statue head, not to be seen from for who knows how long.

Kakashi arrived with Pakkun. He gave the dog a questioning look and it just gave a slight shake of his head. It disappeared in a puff of smoke. Kakashi looked bewildered for a moment at his students appearance, not for the fact that he-now-she was a girl, but for the fact that the near-permanent Henge had dropped. He worried for her health and picked her up and ran quickly back to Konoha. The other rookie Genin were waiting anxiously at Konoha's massive gate. When they saw Kakashi carrying somebody, they became apprehensive as he neared them. They saw him carrying somebody who resembled Naruto. They threw him a questioning glance and all he would say was that they would have to wait for the Hokage to explain everything. They accompanied him to the hospital where the Godaime Hokage, Tsunade, was waiting at its doors. Tsunade ran a diagnostic jutsu on her and confirmed it was just a case of chakra exhaustion. They put her on an IV-drip laced with the properties of a chakra-restoring pill.

After a day, the rookie Genin were summoned to the Hokage's office. Sakura was silently shedding tears and all were looking emotionally down trodden.

Tsunade began, "The reason I have called you here is to tell you that the young female that Kakashi brought into Konoha is actually Naruto."

"NANI?" They all cried in unison.

"You must understand that she was not accepted in the village because of what she contains. Furthermore-"

"-But Hokage-sama, why would she have to hide?" asked Hinata who had already known of her blonde friends predicament?

"She holds the Kyuubi." This statement was met with many gasps and looks of horror. "She was put under the Henge because no one would attack the Jinchuuriki, but it being a girl, they might have become bolder." She said in a grave tone which all the kunoichi understood. "I implore you to see reason and not see her as the Kyuubi." Surprisingly they all nodded and exited her office looking slightly happier.

Naruto opened her eyes to see the white ceiling of the hospital. She sat up and realized that she had been changed into a hospital gown. She blushed at the thought of being naked, something which she hadn't been embarrassed about in a long time. After about ten minutes she got out of bed and was walking out when she noticed neatly folded clothes on the chair next to the door. They had a note attached to them.

Naruto

We know how much you love that idiotic jumpsuit of yours, but we felt that there needed to be a change. Hope you like them.

Rookie nine Kunoichi

She grumbled as she put them on. They were black shorts with an orange skirt, blue shinobi sandals, a fishnet undershirt and a black shirt with a red Uzumaki swirl on it. She shrugged and opened a window. First order of business, get a bowl of ramen. She jumped across the rooftops and landed outside Ichiraku Ramen. She walked in and sat down.

Ayame walked up to her and handed her a menu. "I've never seen you around. Are you new to these parts?"

"Ayame-neechan, it's me, Naruto." Ayame let out a loud exclamation.

"N-Na-Naruto? How is this possible?"

"The Sandaime Hokage put a Henge on me and I lived as a boy for most of my life. I'm really sorry for not telling you guys but he made me swear on my honour as a Konoha citizen that I would not say anything, and I never go back on my word. That's my nindo."

"I really didn't need such a long explanation. The Sandaime told us everything so we could watch over you." Naruto sweat dropped at that.

"Ayame-neechan. Why didn't you ever say anything?"

"Why didn't you?" Ayame replied with a smirk. Naruto sighed and just ordered a large miso ramen with pork cutlets and other toppings. It was brought and she ate. As she was walking out, she bumped into Kiba.

"Sorry about that Kiba. I guess I wasn't looking where I was going." Kiba had a contemplative look on his face before it brightened.

"Oh Naruto, it's you. Sorry I didn't recognize you."

"No need to apologize. It must be kind of hard on you guys to wrap your heads around it."

"Not at all. Personally it explains why you didn't pull away from Uchiha's kiss." He snickered and received a punch which sent him into the wall across the street. Naruto had a tick mark on her forehead.

"I was shocked you asshole! It happened too quickly and before I knew it our lips had already touched!"

"I was just joking! Geez, you're more violent than Sakura." He replied while puling himself from the hole in the wall.

"Sorry, I don't know what happened. I just got really pissed at you. It was uncalled for." She said while bowing. Kiba sweat dropped at that. He was surprised when Naruto held her stomach and bent over. Kiba ran over to her and asked, "What's wrong?"

"I don't know, but get me to baa-chan." Kiba nodded and picked her up bridal style. He ran through the streets of Konoha until he reached the Hokage tower. He barged into the Hokage's office to find Tsunade asleep on her desk with an open sake bottle next to her paper work.

"Hokage-sama! Wake up!" Tsunade grabbed the sake bottle and threw it. Kiba ducked and Tsunade lifted her head to see Naruto sweating and groaning in pain. She told Kiba to put her down on the floor and told him to leave. He hesitated but left.

Tsunade's palm glowed green as she ran a diagnostic jutsu on Naruto. What she found made her sigh in relief.

"What's wrong with me baa-chan?" Naruto asked.

"Nothing really. It's just that it seems sensei's Henge slowed down your hormonal reactions and now that it's been lifted you're going to have your period."

"What is a period, baa-chan?" As Tsunade's explanation began, Naruto screamed. The scream could be heard across the entire village.

A week later, after Naruto had bled for the first time, she came out of her apartment. She was dressed differently this time. It was a red kimono with orange bordering. A tight dark green cloth kept it in place around her waist. She wore the standard blue shinobi sandals and a red clip in her hair to keep the long fringe on her left side out of her face.

She went to the Hokage tower because she had been summoned. She knocked and was told to enter.

"Naruto, I'm glad to see you're feeling better. The reason I called you here was because Jiraiya has requested to take you on a three year training trip. I however see it fit to take you on as my apprentice for the next six months then you may leave for two years because our data shows that it takes at least three years for Orochimaru to be ready to change bodies."

"I see, but baa-chan, what can you teach me?"

"I've done some research and I've found that the Henge that was placed on you disrupted your chakra control. In fact, it's surprising that you were able to do the tree climbing exercise at all, let alone the water walking. I will be teaching you medical ninjutsu, precise chakra control and after the first three months, how to use my strength."

"Why after three months?"

"You will be training under Gai to increase your strength, so when combined with the strength amplification technique, it should be more devastating than my own strength." Naruto's eyes glowed in anticipation and zeal.

"When do I start the training?" Naruto asked.

"Today." Just as Tsunade said that there was an exclamation of dynamic entry and Gai entered through an open window.

"Let's go, Naruto. We have a lot to do." Naruto nodded eagerly and exited, following the speedy Gai to a new training regimen that it in itself, spoke volumes of pain.