The X-Factor

Summary: Orphaned at a young age, Naruto Uzumaki is taken in by Charles Xavier. Will he see a future in which humans and mutants can coexist, or will he be consumed by hate from the rest of the world as he tries to run towards his goal? Naruto x Harem

Disclaimer: Naruto and X-Men are properties of Masashi Kishimoto and Marvel respectively. I make no claims of ownership of the intellectual properties and only want to create an entertaining story using these series. I am also aware that X-Factor is a team name but the context being used is a variable of change.

Chapter 1: X-Factor Origins

Naruto Uzumaki has always been an excitable child who loved playing pranks. The ten-year old boy had been hoping to surprise his father, Minato Namikaze, whom he shared the same spiky blonde hair and sapphire blue eyes with, when the man came home from work. Hiding in the closet near the entrance, Naruto was prepared to jump out and surprise his father who would be returning to their Westchester County apartment in New York any second now.

Minato was usually away from home for extended periods of time for work, and it was always a joy when he could come home to spend time with his family. Kushina Uzumaki, the redheaded wife of Minato and mother of Naruto, was currently in the kitchen preparing a family dinner of ramen for the Japanese-American family. Hearing the rush of footsteps outside, Naruto prepared himself to jumpscare his father as the sounds got closer.

What Naruto didn't expect to see was his father busting into the apartment while clutching his left arm with blood all over his disheveled clothes. There were tears in the man's clothing that consisted of a dark top and matching pants. The most eye-catching part of the top was the emblem on the shoulder of an eagle with spread wings with four spaces between the feathers on each side and two spaces between the tail feathers.

"Naruto! Kushina! Where are you two?!" Minato frantically called out into the apartment as he looked for signs of his family.

"Minato? What's going on?" Kushina asked her husband as she came out from the kitchen and saw a panicked look on her husband's face. "Oh my god! What happened to you? Where did all that blood come from?"

"There's no time to explain! It's not safe here. Where's Naruto?" Minato questioned his wife as his eyes scanned their apartment for any sign of their son.

"I am here!" Naruto exclaimed as he jumped out from the closet.

"Oh thank god," Minato gasped out as he crouched to hug Naruto and pick up his son. "We need to get out here. Now!"

"Minato, what's going on?"

"No time to explain. They're …"

*BOOM*

Minato was cut off when the walls of their apartment were blown apart and the concussive force launched the family of three off their feet.

Lifting his head up, Minato could barely process his condition as he had landed in a prone position as a result of the blast. The ringing in his ears was disorienting and his vision was unfocused.

He saw Kushina's unmoving form off to the side and several figures storming into the apartment. He could barely make out one person carrying the body of Naruto away from him.

"Naruto," the father gasped out as he reached his right hand towards the sight of his son being kidnapped. It was all he could whisper before blacking out from his injuries.

[Unknown]

"Wakey, wakey, Herr Namikaze. Or should I address you by your title, Agent Flash? You have had quite the career and laundry list of interfering with our operations for such an illustrious S.H.I.E.L.D agent," an accented male voice rang out as Minato was regaining consciousness.

Minato could merely groan in response as his mind tried to take stock of his current situation. His eyes rapidly blinked to adjust to the blinding light shining directly onto his face.

With a grunt of effort, Minato attempted to move his body but found himself unable to do so. Recognizing the danger of being restrained, the agent focused his mind to utilize the skill which gave him the title of Agent Flash.

"AUGGHH!"

Minato unexpectedly screamed out in pain as electricity flowed through his body and broke his concentration.

"Ah, ah, ah," the voice taunted as the sudden electrocution subsided.

"Don't even think about using your mutation to escape your predicament. We are monitoring your brainwaves for any indication of you attempting to use your gift of teleportation to escape. Your mind can't focus with thousands of volts coursing through you, can it?"

Minato had to reassess the situation after taking a few seconds to catch his breath. His eyes had finally adjusted to the harsh fluorescent lighting to enable him to get a good look of his surroundings.

Minato found himself strapped to a chair with metal bindings across his chest, waist, and legs. Stripped of his tattered uniform, he was instead dressed in a hospital gown. He also had some kind of metal headband around his head connected to a machine giving out readings which were most likely his brainwaves.

He turned his head and got his first look of his captor. The man was dressed like a surgeon in green scrubs, gloves, a head covering, and a white apron. It painted the picture of a stereotypical mad scientist performing human experimentation. Minato also saw at least half a dozen figures standing around the room dressed in tactical gear and carrying assault rifles.

"I see I finally have your attention Agent Flash," the good doctor mused as he approached Minato while holding a scalpel in his right hand. "You have been a thorn in our side for quite some time now. I hope you are comfortable because you are never leaving."

"What are you after?" Minato asked, hoping to gain insight into his captor's mind as well as stall for time to think up a plan for escape.

"I'm sure you have an inkling of my objectives. Everything is for the glory of HYDRA after all."

"And what would HYDRA want with me?"

"Other than the satisfaction of preventing you from interfering with our operations and taking out one of S.H.I.E.L.D's top agents?" the doctor asked rhetorically.

"To answer your question, research into your X-Gene will yield favorable insight into making our organization stronger. You also stole sensitive information from us, and we would very much like to know what you have done with it. I do hope you will be cooperative as I can make your time with us quite unpleasant. Although, I wouldn't be opposed to disciplining you if you were to be uncooperative. Your family has always been getting in the way of HYDRA all the way back when your grandfather betrayed his German roots by assisting in smuggling Dr. Erskine to the Allies and leading to the creation of Captain America."

"Why in the world would I cooperate with monsters like you?" Minato scoffed at the absurdity of the doctor's words.

"I activated my distress beacon on my way home. S.H.I.E.L.D. should have noticed and sent backup. I just need to hold out until they find me after finding my home ransacked and hope nothing is blocking the signal," Minato thought to himself as he just needed to stall them before his allies would rescue him.

"Hahaha. If you don't cooperate, then I will just have to use our little guest instead," the doctor chuckled as he gestured with his unoccupied hand to the side.

Following the direction of the doctor's hand, Minato's expression switched from defiance into one of horror as he saw his son Naruto being wheeled in while also being strapped to a chair. The little boy's eyes were wide with fear as they looked all around and took in his surroundings.

"Dad!" Naruto shouted out when he saw his father was also strapped down.

"Don't you dare touch him!" Minato growled out as he pulled against his restraints.

"Children are such a blessing aren't they?" The doctor continued to taunt as he took a hold of Naruto's face to force the child to look up into the eyes of their captor. "It's such a shame you had to discover our plans to capture your family. Our own prodigal child X-23 was meant to keep you occupied."

The doctor moved to stand behind Naruto's chair while maintaining his hold on the child's face and stared back at Minato.

"You need to understand that you have no power here, Agent Flash. You are trained to resist interrogation but your child is not. I will be asking you questions. You will answer them. If I do not like your answer, then, well …" the doctor left the threat hanging unsaid as he held his scalpel up to Naruto's right cheek.

"You wouldn't want your son to meet the same fate as your wife, would you?"

"Wait!" Minato shouted as the scalpel got dangerously close to Naruto's eye. "I'll do whatever you want. Just don't hurt my son."

The doctor looked at Minato with glee filled eyes at the proclamation and moved the scalpel away from Naruto.

"Wunderbar! I knew you would see things my way. Love is the downfall of duty after all. Now, I expect you to answer promptly when I ask you a question."

The doctor placed his scalpel down and instead picked up a small remote.

"This handy little remote will manually activate the shockers that are connected to your chairs. Just remember that I can hurt you, your son, or both of you if I find your answers to be unsatisfactory."

Taking a second to acknowledge the remote, Minato could only nod in acceptance at the situation.

"We are going to be well acquainted, Agent Flash. First, what did you do with the documents you stole from the other bases?"

"I turned them over to S.H.I.E.L.D."

"Yes, that much was obvious," the doctor scoffed. "I suppose I should have been clearer. Where is S.H.I.E.L.D located and who currently has the documents?"

Minato wanted to avoid answering this question as this would put his comrades in jeopardy. He shut his eyes to focus his mind in an attempt to conceive a proper answer while masquerading the truth if possible.

However, this action proved to annoy the doctor as an answer hadn't come quick enough. The doctor merely pressed a button on his remote and a cry of pain echoed throughout the room.

"Ahhh!" Naruto cried out in pain as thousands of volts coursed through his body.

"Naughty, naughty. You are stalling too much for my liking and are trying to hide things. I thought we had an agreement," the doctor reiterated as he wagged his index finger at Minato.

"Stop, please! I'll answer you. S.H.I.E.L.D. uses a helicarrier as a mobile base, so I don't know where exactly they could be right now," Minato cried out in desperation to get the doctor to cease the torture.

With a simple click of a button, Naruto's pain ceased but left the boy panting. What the doctor failed to notice was the sight of golden electricity crackling in Naruto's irises and around his body despite pausing the electrocution.

"Somebody, please help us!" Naruto screamed in his mind as he took deep breaths to recover from his ordeal.

[Elsewhere in Westchester County]

A lone man was seated in a wheelchair before a computer console at the end of a walkway in the center of an underground spherical room that appeared to be entirely metallic. He is a bald Caucasian man in his mid-40s dressed in a gray blazer, black shirt, brown pants, and brown loafers with a metal helmet atop his head that was connected to wires that extended down from the ceiling.

This man is known to the world as Professor Charles Francis Xavier, a man with doctorates in the sciences which made him an expert in the fields of genetics, biophysics, and psychology. Unknown to the world, however, Charles Xavier was also a powerful mutant with the gift of telepathy. He was currently wearing a helmet that was part of a mutant detection device dubbed as Cerebro as part of his nightly routine.

Xavier spent much of his time detecting new activations of X-Genes throughout the world to discover emerging mutants so he could eventually be able to reach out to them and invite them to his prospective educational institute to instruct them in controlling their unique abilities.

He believed that humanity was moving in the direction in which more and more mutants would eventually populate the Earth. He was not ignorant of the fear and anger that humanity is prone towards when faced with those they deem to be dangerous. However, due his understanding nature, Xavier truly believed that mutants and humans will be able to coexist with each other peacefully.

"Any fish biting tonight, Chuck?" a gruff voice came from behind Xavier.

Looking behind him, Xavier took in the sight of his fellow mutant Logan, codenamed Wolverine, walking closer while sipping on a can of beer.

Despite standing at a mere 5'3", Logan exuded an aura of intimidation with his muscular physique. Logan's black hair was styled with two distinct spikes on the left and right almost like horns accompanied by thick sideburns. Dressed in a black t-shirt, blue jeans, and brown shoes, his heavily haired forearms were visible to show off his large biceps.

Logan's mutation was two-fold in that he could sprout three-pronged bone claws in each hand above his knuckles, and his body had an extremely powerful healing factor that could practically be considered regeneration that has kept him youthful despite being born over 100 years ago in the 19th century.

Furthermore, he had previously been subjected to human experimentation, known as the Weapon X program, that grafted a nearly indestructible metal known as adamantium onto his skeleton. The experiments had damaged Logan's memory but gave rise to his signature metal bone claws.

"I'm afraid not, Logan," Xavier sighed.

"Somebody, please help us!" A cry reverberated inside Xavier's head just as he was prepared to remove Cerebro from his head.

"What in the world? Cerebro is detecting a recently activated X-Gene" Xavier mused aloud as he closed his eyes and placed his right hand to his head's temple to focus on the voice in distress. Closing his eyes, he began using his psychic abilities to locate the source of that mental cry for help.

The mental image became clearer as Xavier honed in on the holder of the newly awakened X-Gene. He saw the image of a young boy strapped to a chair being tortured with electrocution. He saw the cruel doctor reveling in the pain being caused not just to the boy but to a man with a similar appearance nearby who was most likely the boy's father. Nearby, there were flags with the symbol of a red skull with octopus tentacles.

"Hah," Xavier gasped as he opened his eyes after experiencing the mental anguish of the young boy.

"What happened, Chuck? What did you see?" Logan asked as Xavier came out of his mental dive.

"The new mutant that emerged activated his X-Gene under extreme pain. I saw a young boy being tortured alongside a man I assume to be his father. There were flags with a red skull and octopus tentacles on them."

"HYDRA," Logan growled as he balled his hands into fists and his claws subconsciously emerged due to his anger. This caused him to inadvertently crush his beer can which began leaking all over the floor.

"Where are those bastards, Chuck? I'll rip them to shreds."

"I'm not entirely sure, Logan. What I can tell you is that I felt the young boy's presence in this very city."

"Then let's fire up the X-Jet and rip them a new asshole."

"Agreed. Go get prepared and I'll have Beast prep the X-Jet. I'll guide you both from here."

"Now we're talking. Tell that walking blue Rogaine ad to have us wheels up in ten," Logan stated as he headed off to get changed into his combat clothes.

"Beast, prepare the X-Jet for a mission. You and Logan will be rescuing a young boy whose mutation has just activated from being tortured by electrocution," Xavier psychically messaged to Logan's mission partner.

"Oh my stars and garters! I'll have it ready in five," Xavier heard in response to the mission parameters.

"I just hope we won't arrive too late," Xavier mused aloud to voice out his thoughts.

Ten minutes later, Logan could be seen approaching the X-Jet, also known as the Blackbird, which was a modified stealth jet that was an RS-150 Blackbird obtained from S.H.I.E.L.D. Logan had changed into his Wolverine combat outfit which consisted of a sleeveless yellow top with black accents, matching yellow pants, and a red belt around his waist that had a black "X" as a buckle. He was also wearing matching blue gloves and boots. Furthermore, he had a yellow mask on that left his mouth visible and had two black devil horns attached to the eye area.

The Blackbird's boarding ramp lowered to reveal a blue furred figure that was the so-called Beast who would be accompanying Logan.

Beast was the designated codename for Dr. Henry Philip "Hank" McCoy, a medical researcher in the fields of biochemistry and genetics. Initially, his physical mutation only caused enlarged hands and feet, but he had developed a serum in hopes of suppressing his mutation. The serum had instead accelerated his mutation causing him to grow blue fur all over his body. Standing at 5'11", Beast was only wearing blue shorts with a yellow belt that had a black "X" buckle similar to Logan's as to allow full use of his clawed hands and feet.

"Get us in the air, Bub," Wolverine growled as he boarded as every second mattered for their rescue mission.

"Hello to you too, Logan," Beast mused as Wolverine walked past.

The two got situated in their seats as Beast performed the final pre-flight checks. Wolverine was visibly agitated as he kept tapping his foot while awaiting takeoff.

"How much longer until we're in the air?" Wolverine asked as he failed to get his irritation under control.

"We're taking off now," Beast replied as he pushed a lever forward to engage the jet's engines. "You seem particularly irritable today. Care to share your thoughts?"

"Let's just say this thing with HYDRA dredged up some bad memories. Let's hurry up and save the kid. Chuck will let us know when we're getting close to the psychic distress signal being put out."

A solemn nod was Beast's response as the Blackbird was finally warmed up and began picking up speed before finally taking off into the air.

[Back with Naruto]

"Hah, hah, hah," the young blonde panted as he took deep breaths to take back some semblance of control of his body to recover from his shocking ordeal. Naruto had no idea how long it had been since his capture.

His captor continued to ask his father questions about things Naruto had no idea about. If the doctor didn't like an answer, he would punish Naruto with more shocks.

What was strange for Naruto was it seemed like time slowed down after each shock was applied. Words were becoming elongated when spoken around him and everything appeared to be moving in slow motion. He would snap back to reality and time continued normally, but the duration of the time dilation was increasing each time.

"Anybody, please save us," the boy prayed and begged in his mind to anyone listening.

Naruto's thoughts were interrupted when he heard the doctor speak again.

"I do believe we have made some wonderful progress today," the doctor declared while clapping his hands in delight. "Now, let's take some samples for testing. Shall we?"

The doctor approached a trolley with a table of tools atop it. Various blades and syringes lay upon it as he wheeled the instruments over to Minato.

"Please let us go. Stop hurting daddy," Naruto sobbed out with unshed tears in his eyes.

This gave the doctor pause as this was the first time Naruto had spoken during the entire ordeal.

"Such a good son you have, Agent Flash. His concern for you is touching," the HYDRA scientist mocked. "However, I can appease him for a little bit and pause my fun with you."

The doctor instead chose to approach Naruto and took hold of the boy's chin to force their eyes to meet.

"I am quite curious about the child of someone who has an active mutation. Perhaps your son has a dormant gene that just needs some encouragement to be brought to the surface," he snickered with an unseen smile behind his surgical mask.

The doctor reached over to his tools to grab both a syringe and a scalpel.

"Let's take some samples, shall we?" the doctor eagerly asked.

"Raaghh!"

A grizzly roar rang out from above, interrupting the mad scientist, as a yellow-clad figure dropped down from the ceiling's ventilation shaft.

Wolverine dropped down from above landing a dropkick to the doctor's chest before unleashing his claws to swipe at Naruto's binds.

"Get the kid outta here," Wolverine commanded before crouching low to avoid gunfire from the nearby guards.

He then took off running on all fours at the nearest rifle wielding HYDRA agent. His arms became a flurry of motion as he used his claws to cut through the rifle and delivered debilitating blows to the head.

"Weapon X? Here?!" The doctor exclaimed while prone on the ground as he recognized the rampaging figure of Wolverine. "Sound the alarm! We must not let anyone escape!"

One HYDRA agent immediately pulled out a radio to alert the rest of the base about the threat that had just emerged. In response, the blaring sound of a siren and flashing red lights filled the room as more HYDRA agents dressed in black rushed into the room.

Meanwhile, Beast took advantage of the element of surprise as Wolverine kept HYDRA's attention on himself. All security personnel currently had their weapons trained on the animalistic mutant and weren't prepared for a blue monstrosity to ambush them from above.

"Might I induce a change of heart in you all to stop hurting a child?" Beast rhetorically asked as he began throwing his weight around acrobatically by flipping through the air and stomping on the various gun wielding HYDRA agents.

"You were supposed to wait until I disabled the security system," Beast chastised Wolverine as he continued to manhandle the various black clad gunmen.

"The doc was about to hurt the kid," Wolverine growled out a response as he continued to slice and dice the rifles of everyone he could.

Beast then made his way over to Naruto to put the child over his shoulder and looked upwards towards the ventilation shaft that he entered through.

"Don't worry little one. We're here to get you free. What's your name?" Beast asked to calm Naruto down as well to prepare the young boy to make their escape.

"Naruto. Who are you? What are you?" Naruto asked in quick succession.

"My name is Hank McCoy, but you can refer to me by my nom de guerre, Beast. As for what I am, I am a mutant like yourself," Beast introduced himself.

"Your nom de what and you're a what?"

"No time to explain. We need to quickly get you out of here."

"Wait! We need to get my dad out first," Naruto screamed as he struggled to break free of Beast's hold.

"Don't worry, son. I'm going to get you secured before coming back for him."

As Naruto continued to struggle while held over Beast's shoulder, he noticed a gunman had his rifle trained on his father which Beast failed to notice with his back turned.

"Nooo!" Naruto yelled as the thought of his father dying flashed through his mind. The world seemed to slow down as he heard the sound of gunfire and saw the flash of the rifle's barrel.

As if his body responded to his will and determination to save his father, Naruto suddenly began vibrating in place. His body seemed to phase through Beast's grip and fell towards the floor. Reaching his hand out, Naruto desperately wanted to get his father out of the line of fire.

Suddenly, golden lightning sparked around Naruto's body and in his eyes as his body shot forward with great speed. Less than a second since the shot was fired, Naruto's form blurred from existence from Beast's form and had tackled the strapped body of his father out of the way. The two had ended up slamming into the wall from the velocity of Naruto's tackle, narrowly missing the airborne bullet that shot past their bodies.

Minato stared at his son with wide eyes at what he had just witnessed. His son was a mutant like him. Minato wasn't the only one to be surprised by this development as the doctor had witnessed the interaction while lying prone on the ground.

"Recapture the boy and Agent Flash. Immediately!" the doctor ordered after witnessing the awakening of Naruto's mutation. More HYDRA agents had stormed into the room with their rifles trained on the intruders and began to open fire.

Recognizing the danger, Naruto's mind once again began perceiving the world around him in slow motion. However, this time he had the added advantage of not panicking because he didn't need to get his father out of the way.

Naruto sped forward and pushed the first gunman's rifle upwards before delivering a debilitating one-two punch to the man's crotch. He then sped off towards the next closest gunman while weaving in between bullets. A low kick to the next gunman's legs put them off balance which allowed Naruto to perform a jumping punch into the man's face which created a shockwave on impact. The resulting hit at such a high velocity sent the gunman flying towards other HYDRA agents for collateral damage.

To the eyes of Beast, everything Naruto had just done to the HYDRA agents happened in an instant. The group of gunmen were suddenly displaced from their previous placements and groaning in pain on the ground after receiving blows at supersonic speeds. One gunman was holding their crotch in pain while a group of three gunmen were shoved into a pile against the wall. They all had suffered from broken bones after taking hits from the new speedster.

Nearby, Naruto was also reeling from his actions.

"Ahhh," Naruto hissed as he held his hands in pain. While he had dealt devastating blows to the gunmen, his inexperience in throwing proper punches against the kevlar wearing gunmen resulted in some painful recoil for his hands.

"My word, young man," Beast gasped out in astonishment after witnessing the gunmen become incapacitated in real-time. It had happened in less than a blink of the eye. Walking over to the young man, Beast took hold of Naruto's hands to assess the damage.

"Not to worry. The damage is minimal, and you merely have some sprained wrists," Beast concluded after a quick inspection.

"Dad!" Naruto exclaimed as he went over to release his father from his restraints.

"Ugh," Minato groaned as he collapsed forward after being removed from the restraints.

The aftereffects of the electrocution torture were still felt within his body as he still felt numb and his body wasn't responding to his thoughts. The older blonde needed to be supported by Beast with an arm draped across the furry blue man's shoulder.

"Don't worry. We'll get out of here soon," Beast assured Minato as they began to limp towards the exit stairwell which would lead to the roof and the X-Jet.

Unbeknownst to them, the nearby pile of guards that Naruto previously incapacitated were making moves to prevent their escape with their lines of sight trained on the unsuspecting back of Beast. They could care less about capturing the mutants alive at this point. The humiliation they felt after being taken down by a child, mutant or otherwise, was too aggravating for them to live with.

Shots rang out within the room with bullets flying towards the unprotected backside of the blue furred mutant. Recognizing the danger, Minato's instincts took over despite his weakened state.

"Look out!" Minato yelled as he used all his strength to shove his supporter to the side.

"Dad! No!" Naruto yelled as he witnessed his father take the full brunt of gunfire, saving Beast's life.

"Ugh," Minato grit his teeth as bullets tore through his body, riddling him with holes causing blood to burst out from impact.

Minato collapsed to his knees before falling to his side, succumbing to his injuries. Naruto could not process what he had just witnessed as body began to vibrate uncontrollably. His body generated arcs of golden lightning that caused damage to his surroundings.

"Ahhh!" Naruto yelled as the anger surged through his body. His only thought was to make the gunmen pay for what they had done.

Naruto's form blurred into motion as he threw the full weight of his body towards the perpetrators. A sonic boom was generated from his point of origin as a trail of lightning followed his body.

Naruto had crossed the room in a flash of light and steamrolled into HYDRA agents. The impact sound was far greater this time and sent the group of men through a wall. Not only that, the lightning trail behind Naruto continued to move forward and shot out from Naruto's extended fist, firing a giant bolt of lightning that struck home and further hurt the ones who had caused great emotional pain for the young mutant.

Naruto's body came to a stop after striking the gunmen with his clothes having caught fire due to the great speed his body was moving at. The young boy's eyes began to feel heavy after expending so much energy as he started to lose consciousness. The last thing his mind registered before fading to black was Beast moving towards him while carrying his father's body.

Beep beep beep

The rapid beeping sound of an EKG machine was the first thing Naruto's mind perceived as he slowly returned to consciousness. There was a faint sound of classical music playing in the background with an operatic female voice as the young boy tried to open his eyes.

"Ugh," Naruto growled to himself as he forced his eyes open and had to rapidly blink to take in the intensity of the fluorescent lighting.

"Ah, welcome back my young friend," the jovial voice of Beast rang out.

Naruto's eyes were finally focused and the familiar blue form of Beast came into view. What Naruto didn't expect was the furry mutant to be hanging upside down by his large feet clinging to a pipe system connected to the ceiling.

Naruto attempted to sit up in his bed but had to clutch his head from the throbbing pain he felt.

"Ow, my head. Could you turn off the music?" Naruto groaned out.

"Are the melodic melodies of Mozart not scintillating your synapses, my young speedster?" Beast rhetorically asked as he released his feet's grip on the pipe and landed down on the ground.

"What?" Naruto groggily asked as he took note of Beast's appearance who was currently wearing a white lab coat as well as a pair of black framed glasses.

"You shouldn't push yourself so soon, young man. You've been unconscious for the last twelve hours and needed a lot of nutrients in the meantime."

"What do you mean?"

Beast merely gestured to the floor to Naruto's left.

Looking to the side, Naruto noticed a tube connected to his left arm that led to a metal stand with an IV bag. On the floor beside his bed were several emptied IV bags as well.

"Your mutation that grants your immense speed seems to have also sped up your body's metabolism. You are burning through your body's energy too quickly and will most likely require a significant increase in calories for your daily diet."

As if to prove Beast's point, the blonde boy's stomach began growling audibly for the two to hear.

"I'm hungry," the boy moaned as he moved his hands to clutch his stomach.

"Hahaha," Beast jovially chuckled in response. "It's just about lunch time. Let's go get you some food."

Reaching over to help the young boy out of the bed, Beast accompanied Naruto out of the medical room. The outside hallway had walls of metal that looked like chrome and each door they passed were marked with a large 'X'. Their short walk led them to take an elevator in which Beast pressed the button indicating an upward facing arrow.

After a quick ride together inside the elevator, the doors opened up to a hallway adorned by numerous paintings and walls that looked to be made out of dark colored wood. Riding up meant Naruto had previously been in an underground and hidden medical room.

The duo continued their stroll into a nearby dining room which had large windows that allowed sunlight to illuminate the room, high ceilings, and a long table that could comfortably seat twenty people at least.

"Where are we?" Naruto found his voice to ask as he took in his surroundings. Everything around practically screamed a rich lifestyle at him.

"We are in the home of a dear friend named Charles Xavier. He will explain why we went to rescue you."

Snikt

The sound of scraping metal caught Naruto's attention as he turned to see Logan with his cowl pulled back along with the familiar yellow suit and claws. The older man had used his claws to stab into three sausages to eat off of while he held a newspaper in his other hand.

"Well, well, look who's up, bub," Logan mused aloud as he had caught Naruto's staring.

"Ah, I assume you remember Logan, or Wolverine as he is called in the field, from our previous encounter?" Beast asked while guiding the blonde towards the table.

Logan merely nodded his head towards the two in acknowledgement before taking a bite out of each of his three sausages.

"You said my mutation makes me hungry. What does that mean?" Naruto asked as he took a seat at the table and looked up at Beast.

"I'm sure you must have a multitude of questions. Let's wait for our gracious host to arrive and explain things to you," Beast responded while taking a nearby seat across the table from Logan.

"Thank you for waiting for me," a voice rang out through the minds of the three seated at the table which alerted them to the arrival of Professor Xavier wheeling into the room.

"Hello, young man. I am Charles Xavier. Welcome to my home."

"Why did I hear you in my head? Why am I here?" Naruto asked after being startled by the sudden voice in his mind.

"You've been brought here because I heard your cry for help with my telepathic abilities. The three of us are mutants, just like you."

"What's a mutant? Beast called me that before."

"A mutant is someone who is born with a genetic mutation called an X-Gene. This special gene causes their bodies to develop abilities that regular humans are unable to through mutations.

"For instance, my ability is telepathy. I can read the minds of others and psychically send thoughts to others as well," Xavier demonstrated as he placed his right hand up to his temple.

"As you can probably guess, my mutation has given me claws, large feet, as well as getting my body covered in blue fur," Beast chimed in.

"You've seen these babies in action already," Logan mused while waving his three-pronged claw around before finishing off his sausages.

"As I was saying, the majority of mutants develop their abilities usually upon puberty. However, this can vary from person to person as I have known some to have developed their mutations from birth or even in their late twenties. The emotional and physical trauma you experienced during the time of your capture most likely pushed your body to activate your X-Gene to give you the ability to protect yourself," Xavier continued on.

"You mean my speed is my mutation?" Naruto asked as he looked down at his hands and imagined himself moving at superspeed.

"That's right. You're lucky that I make it a habit to detect new and emerging mutants because I believe that one day there will be a large population of mutants inhabiting this planet. I plan to open my home to young mutants as an institution of learning to help teach control over their powers. History has shown us that the world is not a kind place, but I genuinely believe that coexistence between mutants and mankind is possible. I would like you to join us, Naruto."

Naruto looked down as if to contemplate his choice. What he experienced in the last few days turned his life upside down and now a stranger is inviting him into their home to learn to control his newfound abilities. However, another haunting question came to mind for the young boy.

"What happened to my dad?"

The three adults could only look at each with somber looks before turning back towards Naruto.

"Your father has unfortunately perished after succumbing to his injuries when he pushed me out of the line of fire," Beast responded as he closed his eyes in sorrow. "Your father was a brave man, and I owe him my life."

Naruto's eyes welled up with tears as he realized the severity of his situation. He had no family that he knew of and has now been orphaned.

"What do I do now?" Naruto sobbed out.

Seeing the distraught child before him, Xavier wheeled over to place a hand on Naruto's shoulder to console him before speaking up.

"I think the first thing we should do is honor your father's sacrifice with a proper burial. We recovered his body and wanted to speak with you first before making any decisions."

"What about my mom?"

"We …"

"Someone's coming," Logan interrupted as he got up from his chair to look out of a nearby window in the direction of the driveway. "I hear helicopter blades approaching."

The sound of whirling blades grew louder as a black helicopter came closer and closer towards Xavier's mansion-like home. Landing on the front lawn by the fountain near the front door, a dark skinned man with a shaved head, an eye patch covering his left eye, and a black goatee exited the helicopter.

The man wore a gray trench coat over a full-length black bodysuit with knee-length black boots, white gloves, and a gun holster strapped to his left chest. Walking up to the front door, the man knocked on the door which seemed to echo throughout the building.

The door opened to reveal Xavier who looked perplexed at the stranger on his front doorstep.

"Yes, may I help you?" Xavier opened up the conversation after taking a moment to assess the visitor.

"Hello, you must be Charles Xavier."

"I am. Who are you good sir, and what brings you to my humble abode?"

"My name is Nick Fury, and I'd like to speak with Naruto if you wouldn't mind allowing me in."

"I do believe you're mistaken, Mr. Fury. There's no such person by that name here. Good day sir," Xavier offhandedly replied before attempting to shut the door in the man's face.

"I think we both know who I'm referring to," the man interrupted as he stuck his foot out to prevent the door from closing. "If it helps, you can have Beast and Wolverine at your side. You can even read my mind if that helps."

Xavier's face immediately shifted to a more stern and serious expression after hearing the words leave Fury's mouth. Rolling his wheelchair back a few feet, Xavier gave space for the unexpected arrival to enter before shutting the door afterwards.

"Nice place," Fury mused as he took in the surrounding hardwood architecture and art within the foyer. "Is there a place where we can all speak together?"

Xavier raised a hand to direct Fury towards the dining room which had been hosting the four mutants previously. Entering the room, Fury was greeted with Wolverine's claws in his face and the masked mutant growling.

"What do you think you're doing here, bub?"

"I'm here because you gentlemen have an asset of S.H.I.E.L.D's on the premises," Fury nonchalantly answered and not at all afraid of being turned into a shish kabob.

"An asset?" Beast asked while still seated at the table.

"Minato Namikaze aka Agent Flash."

"That's what the mean man called my daddy," Naruto's voice spoke up.

"You must be Naruto. Your dad worked for me at the Strategic Homeland Intervention, Enforcement and Logistics Division otherwise known as S.H.I.E.L.D. We're dedicated to protecting the world from threats, and your father was one of our best agents. Unfortunately, information on his family was discovered by HYDRA which led to the attack on your apartment."

"So what business do you have with us?" Xavier questioned.

"Well first of all, we would like to properly lay to rest one of our own. I'm here for Minato's body. We've already recovered the body of Kushina Uzumaki."

"You have my mom?" Naruto asked with hope in his voice.

"That's right." Fury reassured Naruto by crouching down on one knee and patting the young boy on the head. "They'll be buried together and you can visit them."

"Thank you," Naruto nodded in gratitude.

"Second point of business is what will be done for Kid Flash here," Fury continued as he referred to Naruto.

"We've scrubbed the security footage and data in the HYDRA base, so his abilities shouldn't be known to the rest of the organization. However, with no living relatives, Naruto will have to go into the adoption system or he can stay with S.H.I.E.L.D and one day become an agent."

"You're talking about drafting a child!" Beast raised his voice at the outrageous option that Fury was suggesting.

"Is that any different than what you plan to do with young mutants?" Fury countered. "We are well aware of your kind and the danger you so-called homo superiors present to us homo sapiens as more mutants emerge. If you are the next step in evolution, then our kind will die out like the neanderthals before us."

"I believe in coexistence," Xavier sternly replied. "Mutantkind and humanity will be able to live together in peace. Our kind are not a danger to you."

"Can you speak for all of your kind? What would your old friend Erik Lehnsherr say to that?" Fury fired back.

Xavier was taken aback at the mention of his old friend. Taking a second to compose himself, Xavier processed his thoughts before voicing his opinion.

"While I can not speak on behalf of Magnus, I believe the next generation have the potential to be guided in the right direction. I'm hoping Naruto here will be the first example of that and be allowed to stay here."

"Ummm, I want to stay here," Naruto spoke up. His face was determined as he gathered the courage and strength to declare his intentions. His eyes were focused and stared right back at Fury.

"I want to make sure people don't get hurt and to protect as many as I can."

The three older mutants all smiled at Naruto's declaration before collectively looking at Fury for his response.

"Quite the strong impulse you have there, son," Fury smirked after taking in Naruto's words.

"Godspeed then. I suppose we're done here. One more thing. A pension for Minato's service will be paid out for the rest of Naruto's life. Consider this a gift. Just don't forget that we'll be watching."

With his final piece said, the government agent walked away from the one who would eventually become a pillar of mutantkind in the future.

The four remaining mutants watched on in silence as Fury stepped back into the helicopter which took off into the horizon. The silence was eventually broken when Xavier turned to address the youngest addition to their motley crew.

"Well, this has certainly been an eventful last few days for you, but I would like to formally welcome Naruto Uzumaki as the first student of the Charles Xavier's School for Gifted Youngsters."

Xavier and Beast clapped their hands together to congratulate their new charge officially joining them while Logan merely nodded his head in recognition.

Naruto looked up at the older mutants before breaking out in a large smile.

"I'll be the best and won't let you down."

[Weeks Later]

Naruto's life had settled into a routine over the last couple of weeks since activating his mutation. After attending a brief funeral service for his parents alongside agents of S.H.I.E.L.D, Naruto began learning about his abilities in earnest.

Professor Xavier and Dr. McCoy were in charge of his compulsory education while Logan was his instructor in learning to defend himself. Furthermore, Hank played the role of a researcher when monitoring the data collected regarding Naruto's abilities and ensuring Naruto's health.

For instance, Naruto sometimes needed upwards of ten thousand calories a day depending on how often he used his abilities. His hypermetabolism burned through his body's energy too quickly which also made it difficult for Naruto to build muscle. Hank has since made the decision to tailor a diet for Naruto's growth supplemented with special calorie protein bars that were developed as emergency snacks.

Training in the use of his mutation was centered around safely using speed for himself and others. Testing had shown that Naruto's body manifests a protective aura when using his powers which is the reason why his skin wouldn't peel off when moving at such high speeds. This aura even extended to objects in contact with Naruto, so it is possible for Naruto to carry others at high speeds as well.

It wouldn't bode well if Naruto ended up killing those he tries to protect when moving them out of harm's way. However, Naruto did need to train himself to have a gentle touch when carrying others. This was practiced by having Naruto pick up and transporting eggs to be dropped off when moving at his supersonic speeds. Those eggs also doubled in purpose as being part of Naruto's high protein diet.

Another core aspect of his training was properly changing direction and coming to a stop. The dozens of pairs of sneakers with burnt soles can attest to the difficulty that Naruto had when coming to a stop on a dime when reaching his top speed. The solution was for Hank to create boots as well as a uniform for Naruto to wear that were both heat and abrasive resistant. The clothes had an added benefit of not catching fire as to prevent a possible wardrobe malfunction.

Currently, Naruto was clad in a black bodysuit with yellow accents that highlighted the middle of the torso as a vertical stripe, yellow gloves, yellow boots, and a yellow belt with a belt buckle that had a yellow 'X' with a red background. His head was also covered in a black cowl that left his mouth exposed and yellow goggles to keep the wind out of his eyes when running.

Naruto at the moment was practicing his two most difficult abilities in the Danger Room, a training room built underground the mansion meant to challenge the trainee through the use of traps, projectile firing devices, and mechanical dangers.

The most tiring of his given abilities were phasing through solid objects, such as when he escaped Beast's hold back in the HYDRA base, and the ability to direct the bio-electricity generated when running by throwing it like a bolt of lightning at adversaries.

Vibrating his body at a specific frequency would allow Naruto to pass through solid objects but extended use was especially tiring for the young speedster. It has led to bloody noses for him in the past. Throwing lightning has been a matter of fine tuning his aim as he needs to maintain focus when moving at high speeds to direct the lightning at his target.

However, Naruto was nothing if not determined to master his abilities to prepare for the future. He needed to be ready for when mutants would become common knowledge to the world as currently the world was mostly ignorant to their existence. His thoughts were interrupted by the sound of Beast coming over the intercom.

"Take a breather Naruto and come greet our guest."

Taking a death breath and a moment to straighten his posture, Naruto looked towards the opening door which revealed two people entering the Danger Room. Professor Xavier was accompanied by a young Caucasian girl with shoulder length velvet red hair and shimmering emerald green eyes.

The girl looked around the room before settling her gaze on Naruto's form. She looked a bit uncertain as Naruto approached her but let out a sigh of relief when the boy removed his cowl to greet her with a bright smile.

"Naruto, this is Jean Grey. She will be staying with us as a student from now on. Jean, this young man is Naruto Uzumaki," Xavier introduced the two children to each other.

"Hi," Jean shyly greeted as she tucked a strand of hair behind her ear.

"Hi. I like your hair color," Naruto responded as the eye-catching red color of Jean's hair reminded him of his mother's.

Not expecting the compliment, Jean's face flushed red but had the added benefit of getting the young girl to crack a smile.

Little did Naruto know, this was the first of many encounters he would have as he fights for coexistence between mankind and mutantkind.

Author's Note: Thank you for taking the time to read the first chapter of my new story. I have always wanted to see more speedster Naruto stories existing. I have been agonizing over writing this as to bring this idea I had into creation before I get back to updating my other story. Authors who can consistently juggle and maintain updating multiple stories have my respect. Anyway, I hope you enjoy this and future chapters of my Naruto/X-Men story. It will mostly use X-Men Evolution as a base as that is what I grew up watching, but I will mix in inspiration from other incarnations when I can such as the 90's X-Men animated show and other Marvel properties. If you want to interact with a bunch of neat writers and authors, you can catch me being pretty active in Aizenthegoat's Discord server as well as Grumpywolf's server. I will leave links below.

Catch you all later.

The Goat Server: /k2fnemnSGe

Grumpy Fanfiction: /xbT9YjRQJw