An: Based on "Fox Queen" written by flashfox tyrell05 I wanted to write it I couldn't get this story out of my head given how Fox Queen intrigued me so much that it made me want to do another Naruto X Alien Crossover so I'm giving this story a shot I promise you, you will enjoy my version of "Fox Queen" with a reference of "Abomination" but instead I dubbed it as "Kitsune Empress" I hope you enjoy it cause there will be powerful strong Naruko and I'm also adding a little Species or star craft to the story like give Naruko Sarah kerrigan's powers and element like bloodlines I will explain more when I reach a certain part of the story or chapter

parings undecided or I could make it a flat out harem.

Story Title: Kitsune Empress

Summary: kidnapped and experimented on, a child will become a apex predator like no other. The creature will become a woman in the eyes of the world however she would forever be a monster but something greater and terrifying, Naruko Uzumaki will show the world the might and strength of a new empress.

Rated: M.

Parings undecided might make it a harem.

Prologue.

" Oh my kami..." Sarutobi Hiruzen whispered with horror, disgusted in what his old rival had done Beyond what he had been prior. Having finally found a piece of hard evidence against Danzo, The sandaime had led an aggressive and offensive investigation against the old war hawk eventually getting enough evidence to lead a raid on the man's Root facilities. Among them was a laboratory hidden deep within the hokage monument. After infiltrating the place with several dozen Anbu that were only loyal to the Hokage himself and handful of jonins the hokage had hand-picked for the operation, they struck, arresting those they could and killing those they couldn't. Several of them had committed suicide, biting down a poison tooth to end their lives before they could be questioned.

But that wasn't what sickened "The Professor"

It was the occupant of the liquid-filled glass obelisk set before him.

Appearing to be between the ages of 6 or 7 was a child with three whisker marks on each cheek, black hair, blonde kitsune ears with black tips on the child's head, eyes were colored obsidian cat like with black slit puplis, nails were pointed and sharp colored black, skin was pale and what else did the child had?. A six foot tail that was black with a blade at the end of it, five digit hands too.

Hiruzen couldn't believe what his old eyes were seeing this child looked like his surrogate grandson Naruto Uzumaki except.. this Naruto he was looking at now in the container was a female.

" Is that... No... It can't be..." Itachi Uchiha muttered in shock behind his anbu weasel mask looking at Naruto as he approached removing his mask from his face to see the person with both eyes.

" Naruto..." Hiruzen whispered, still shocked and couldn't believe what his old rival had done to the child he once considered a surrogate grandson.

"Hokage-sama, we must let her out!" Exclaimed Yugao who was code named Neko while Hiruzen glanced at the red button that said 'release' across it in bright yellow lettering and flipping the clear Plexi glass cover and and pressed the large button with his hand as the liquid in the container was draining with itachi now opening the container to pulling Naruto out who was still sleep as if she was in a coma. The uchiha cradled naruto in his arms looking at his comrades and Hokage until Kakashi and his squad of anbu appeared.

" Hokage-sama Danzo has escaped we failed..." He said bowing respectfully towards his leader with the anbu doing the same while Hiruzen growled with a scowl on his face that his old rival had escaped.

" Orders sir?" Asked Yugao with hiruzen turning to her.

" Find what else Danzo has been hiding and keeping down here and find anyone else who was a victim in his cruel experiments until you do destroy this laboratory and everything in it!" Spoke Hiruzen with furious anger with his Anbu and Jonins nodding leaving the Hokage with Itachi and Yugao.

" What are we going to do about her Hokage-sama? she seems to be in a coma..." Said Yugao with him now sighing sadly looking at Naruto.

" We will return her to the village and take her to the hospital... I may have to contact Tsunade if our medics fail to wake Naruto out of her coma..." He said grimly

" What of Danzo?" Itachi now spoke

" He will be labeled as a traitor for the crime he has done..." The Hokage replied with venom still furious at his old rival.

" Let's go... It seems I have to start a meeting with the council and inform them this however Yugao and Itachi you two take Naruto to the hospital and guard her when the meeting is over I will come to the hospital." He said with them nodding as Itachi carried Naruto in bridal style walking out the lab with Yugao following him.

( Council chamber)

Sarutobi Hiruzen had summoned both sides of his council, the shinobi council and the civilian council along side of them were the elders the Hokage's advisors Homura and Koharu the only elder missing was Danzo.

" Thank you all for coming on such short notice.. this is an emergency meeting which is why I have summoned you all here." Hiruzen said in a serious tone looking at both councils who tensed under his tone.

" What seems to be the problem Hokage-sama?" Asked a civilian council member while the fire shadow sighed at what he was going to say.

" The reason I have summoned you all is to discuss an S-rank secret and if it leaves this council chamber you will be killed on the spot.. do I make myself perfectly clear?" Said Hiruzen with seriousness in his tone while leaking killer intent to get the message through both councils as they flinched at his tone and they knew if they spoke of the secret they would be killed.

" What's so important about this secret Hokage-sama?" Asked Fugaku Uchiha who raised a eyebrow and was anxious about the secret.

Before Hiruzen could speak Homura interrupted him by saying.

" Where's Danzo? it's not like him to be late?" Spoke the old elder while his friend Koharu wanted to know where was the old warhawk.

" This discussion is very much about Danzo and what he has done." Said Hiruzen with venom in his tone at the mention of his former team mate as both councils turned to him looking tensed.

" What has Danzo done Hokage-sama?" Asked Shikaku who had a feeling the old war hawk had done something horrible and from the way the Hokage said Danzo's name might confirm his suspicion.

" Danzo has committed a treasonous crime and is declared a traitor for what he has done tonight I have discovered that not only he still had Root active but has been keeping orphans in his root facilities molding them into emotionless root anbu. But that's not all he did... he has done what would Orochimaru be proud of... he has experimented on a child." Said Hiruzen with a cold tone earning shocked faces and gasps from everyone in the council room as Hiashi Hyuga now ananswered.

" Who is this child did Danzo experimented on Hokage-sama?" The Hyuga Clan head asked while many in the room wanted to know as well.

" The Child he has been experimenting on was none other than Naruto Uzumaki" He replied with sadness and disgust for what Danzo did.

Both councils looked shocked and horrified.

" Did he tamper with the kyubi's seal?" Asked Inochi Yamanaka

" I do not know... I don't know what he has done but I managed to find this file he documented about Naruto" The old kage said pulling out a file from his robes that had everything about Naruto and on the front of the file was labeled in red handwriting that said. 'Project Empress' laying the file on the table everyone looking in shock.

" Project Empress?" said Shikaku in confusion looking at the file something told him that Danzo may have done something else to Naruto .

" Yes... Naruto is not a male anymore... he is a female now..." muttered Hiruzen making the council gasp

" What the Hell did Danzo do? he turned the pup into a female now?!" Spoke Tsume Inuzuka with shock to make sure she heard that correctly with Hiruzen nodding.

" Where is she now Hokage-sama?" asked Choza while the old kage answered

" She is now being held in the hospital guarded by Weasel and Neko as of right now I will double more anbu to look after her and I myself will check on her... she seems to be in a coma I'm depending on our doctors at the hospital to wake her from her coma and if she doesn't I may have to summon Tsunade Senju back to the village to wake her and summon Jiraiya as well to check the Kyubi's seal to make sure Danzo didn't tamper with it or damage it due to experimenting on her..." He said with many looking a little relieved about what he said.

" This meeting is adjourned and remember this is S-ranked if what was said in this chamber mentioned out in the village you will be put to death understand?" He said getting nods from everyone as he nodded as well.

" Good." He said now getting up from his seat now leaving the council room to go to the hospital.

( Elsewhere out on the borders of Fire country far from konoha)

In a hidden Base where a old man was with a cane, a bandaged face that covered his right eye and his arm in a sling. besides the old man were a group of anbu that had blank masks and the Kanji for Root on their masks as the old man spoke.

" Sai." he said while a pale boy stepped forward to the old man and got on one knee in a bowing position.

" Yes Danzo-sama" Sai replied in a emotionless tone looking up to his master.

" I have a special task for you... and I entrust this mission to you." Danzo stated with a stoic expression.

" What is your bidding Lord Danzo...?" Sai asked.

" You are to return to konoha and be a spy for me I want you to let me know what happens in the village while I am in exile" Danzo said with Sai Nodding

" And I also want you to keep a sharp eye on Project Empress inform me of what she does and her development..." He said with the pale boy nodding.

" As you wish Danzo-sama it will be done" Sai Replied.

" Good now go and do not fail me..." He said in a harsh tone as the boy rose up and went on his way back to Konoha

" What should we do Danzo-sama" Said Fu looking at his master.

" We are going to a new base of operation... strengthen our forces and remain hidden until the time is right to show ourselves..." He said looking up at the clouds

" What of Project Empress?" Spoke Torune

" Do not worry if she were to find out and seek revenge for what I did to her I have a fail-safe incase she lashes out on us I placed a loyalty seal on her so that I could control her she will only listen to me and no else once I have that seal activated." He said with a grin

" Let's go... we must keep going it won't be long till Hiruzen sent hunter nins after me." He said walking now with his army of root behind him.. he hoped his plan will go all he needed to do was wait when the time comes and if his former team mate Hiruzen were to pass away he and his root will reclaim konoha and mold it to his image with Naruto at his side will be a weapon for konoha like he always wanted then rise to the top by making konoha the strongest village and him becoming The new 5th Hokage or 6th Hokage. But first things first he needed to find himself and his root a new base for them to hide in exile.

( Konoha Hospital)

In the Hospital Naruto was in a room still in her coma while the Doctors and Nurse were checking on her like the Hokage ordered though the Anbu were guarding the door while Itachi and Yugao were inside the room watching the doctors as they waited for the Hokage to come and meet them.

He walked in while the doctors, and nurse alongside Itachi and Yugao bowed to him as the first doctor came to him she was a female as he spoke.

" How is she doing Doctor?" he asked.

" She's stable and some what healthy however Hokage-sama there seems to be a problem." She answered to her superior

" What's the problem?" he wondered with a frown

" We can't get her out of her coma we tried everything the only one with the skill of healing and awaking her from her coma would be Tsunade Senju" The doctor said as she held her clipboard writing notes.

" I see... very well I will do my best to contact Tsunade and get her back in the village anything else I need to know doctor?" He said with a sigh.

" We did a few scanning on her Hokage-sama her chakra is very different and her blood is also green and acidic..." She explained while he and the others in the room looked shocked Why is Naruto's blood acidic and green.

"Anything else?" He asked with a look of worry on his face.

" Not so far milord we are still checking on her to see what develops" She replied.

" Very Well... I will take my leave keep me posted on what happens to her" He said with her nodding as he turned to Yugao and Itachi with them bowing.

" You two are in charge consider this a S-rank do not let anyone in this room but me and her doctor understood?" He said with them nodding.

" Good I'm going to my office and make it my business to contact both my former students about this matter" He said walking out the room leaving Itachi and Yugao and the doctors alone with Naruto

Unknown to anyone that Naruto herself twitched and shivered while she was in her coma.

To be continued.

AN: I hope you all are pleased and enjoyed this story like I said couldn't get it out of my head after reading "Fox Queen" so just so you know in this Story I'm mixing Aliens/ Species/ and maybe a little star craft like give Naruko Sarah kerrigan's powers and Eve's power or personality. since she's already half Xenomorph with Queen status but instead she will be an empress since I made her a combination of Eve, (species), Sarah Kerrigan ( Star craft) and Xenomorph Queen/ Empress (Aliens) . until next time in a few days Elf Kitsune is coming up I haven't forgotten so are you later.