Author Note: I hope you like the story.
Disclaimer: I don't own Pokemon or Naruto.

Please enjoy!

X.o.X.o.X.o.X.o.X.o.X.o.X

Humans are untrustworthy.

Mewtwo hated every single one of them. They had been ignoring her plea, relentlessly testing the limits of her power through inhumane methods. Those vile tests were beyond cruel, yet efficient. It compelled her to measure her strength. Mewtwo would be confined in a chamber and flooded with tremendous electricity; her only way to prevent being murdered was to use her insurmountable psychic prowess to shield herself.

However, the moment Mewtwo let her guard down, the humans would enhance the intensity of the electricity to shock her unconscious. She would wake up from severe migraine and agonizing bruises before repeating the tormenting process once more. It was a routine to the humans, but to her, it was a never-ending hell.

"H-Humans… they are all monsters! They care nothing but to use my powers for their sick pleasure!"

There was something peculiar that confounded Mewtwo though. A boy with sunglow hair would sneak into the facility every night and read books to her. At first, Mewtwo thought the boy was mocking the fact that she was kept in captivity, but she assumed wrong. The mysterious boy would give her the most benevolent and innocent smile when he told her stories. It was from there she realized that he, too, was a by-product of experiments.

Mewtwo hated to admit it, but she grew fond of the boy. He was unlike the rest of those despicable humans who tortured her. He was different, just like her. An anomaly in the ecosystem. He didn't look at her with eyes filled with prejudice and contempt. He didn't view her as an apocalyptic weapon. Hell, he didn't even know what she was. Couldn't really blame the child. After all, Mewtwo didn't have an answer to that question either.

"So what am I? A deviant who is chained in this godforsaken cell for the rest of my life? A puppet that will always be tangled with strings? A monster born to be destruction incarnate? Am I a mistake?"

"Nope, I don't quite agree with you. Well, I don't think you are any of that."

Mewtwo blinked in surprise. "Y-You can hear me? But how?"

The boy placed a finger on his lips, as if contemplating for a plausible answer, but failed. Scratching his head sheepishly, he let out a light-hearted chuckle. "I don't know. I guess that's the reason why I'm stuck here with you. As for your questions earlier. I don't think you are a deviant, because if you are, then I am too. Not that I know what deviant means. And you certainly aren't a puppet. I mean… Pinocchio is made out of wood. You don't look like wood to me."

Resisting her urge to sweat-drop at the boy's naivety, Mewtwo sighed. She was suspended in a tank, submerged with fluids that keep her tranquilised. The humans were cautious, ensuring that she was constantly enervated when she was not undergoing any tests. "I always wanted to ask you something."

"Fire away!" The boy beamed.

"Why do you always come here? Do you not fear me?" Mewtwo asked with a soft and feminine eloquence.

"Fear you?" Folding his arms and tilting his head in confusion, the child merely arched a brow comically and mused. "Why would I? You look pretty to me. Besides, I don't like staying in my cell. It makes me… sad. Talking to you makes me happy."

Mewtwo was… speechless. What did the boy mean by her being pretty? Was that supposed to be a compliment? Did she look physically appealing? And why was she feeling strange all of a sudden? It would seem like asking the boy questions lead only to more questions. "I don't understand. Talking to me makes you happy? How so?"

The boy shrugged. "Beats me. It's just… I feel like I'm at home when I talk to you. I don't know how to explain that feeling. It's like nostalgia. In all honesty, I don't really know what a home is. I spent my whole life here. I won't really call this place home, but talking to you- Uh! Haha! I'm babbling again."

Mewtwo pondered. Home? What is a home anyway? Would she feel safe and comfortable in a home? What can a home possibly offer her? Security? A pleasant life? Did she even have the luxury to consider such things? No. Mewtwo prided herself as a pragmatic individual. Home was a far-fetched idea. A fairy tale. As long as she was trapped in this penitentiary, there was no home. There was only hell.

"How did you manage to sneak your way here?" Mewtwo pried, trying to divert the topic to something buoyant.

The boy pumped his chests out with a confident vigour and grinned toothily. "What can I say? I'm a genius! The guards are always reckless and I remembered the schedule of their shifts. So, I managed to steal one of the guard's key, make a replica with the broken tiles in my cell and voila! I can only go this far though."

His shoulders slumped. "This place is a maze, I tell ya. All the corridors look alike. Sometimes, I got lost trying to find my way back."

Mewtwo narrowed her eyes, discerning the boy's words in deep scrutiny. He was not deceiving her, that's for sure. It didn't take a telepath to tell that the boy was incapable of deceits. Then that only meant one thing. The humans were using the boy to further study her. The facility was renowned for being impenetrable and its paramount security force. There was no way the boy was allowed to roam the building without being detected.

They were being watched.

"So why did you choose to talk now?" The boy queried. "I mean, you never attempt to-"

"Leave." Mewtwo averted her gaze. "You don't belong here. And from now on, don't ever come back here."

"B-But-"

"I said LEAVE!"

Tears threatened to burst from Naruto's eyes and he nodded dejectedly. The boy thought he had made a friend. He even managed to make his silent friend talk, but he had screwed up. He didn't know what went wrong. Was it something he said? Probably. He didn't really have much social skills to begin with. Wiping his tear and stifling his sobs, the boy turned around. "I'm sorry for bothering you."

The boy strolled hurriedly to his secret passage and climbed his way out.

Mewtwo caught a glimpse of sorrow in the boy's eyes when he left. Tribulation and guilt were stirring in her stomach. She empathised with the boy; she really did. When she was young, her handlers had tried to befriend her. In her desperate attempt to find solace for her loneliness, she took the bait, not knowing that she was being deceived. The humans had betrayed her trust and exploited her imminent rage to assess her powers.

She didn't want to hurt him like that, but she had to. She would not allow the humans to use the boy to get to her. Never, not in this life or the next. The truth was… she really did enjoy the boy's company. It gave her some semblance of peace in this hellhole. His presence gave her a purpose to live. He motivated her to endure and muster up the will to not take the easy way out and commit suicide.

"Forgive me." A lone tear of poignant despondence fell from her eye.

She didn't even get to ask for his name.

X.o.X.o.X.o.X.o.X.o.X.o.X
(Two weeks later…)

Mewtwo groaned as she struggled to withstand the incessant pulses of electricity directed at her. She had sustained her psychic barrier for three hours straight, but the humans were unyielding. They kept pushing her and pushing her, all the while having a malevolent smirk plastered on their faces. It disgusted Mewtwo. How terrifyingly ruthless can humans be? It frightened her to think that the humans had every intention to analyse her ungodly powers, even if that means killing her.

She noticed however that the humans were not paying much attention to her. They seemed distracted. Curiosity piqued, she heightened her telepathic strength and eavesdropped on their conversation.

"Have you heard? The director plans to depose off the brat."

Mewtwo arched an absent brow. "Brat?"

"Brat? You mean Naruto? Why? Didn't he want to study him a bit longer?"

"Yeah, that's the one. The little rascal thought he had everybody fooled. We know he had been crawling around the building every night. And he thought we didn't know about his escapade. The director thought he could communicate with Mewtwo and informed the guards to ignore him."

"So why the sudden order to end him? He can understand Pokemon, can he not?"

"Apparently, the kid failed to bond with Mewtwo. The director found him useless. We have already extracted his DNA and stored blood samples back in the labs. He is on his way to the guillotine as we speak."

No! It couldn't be! Mewtwo panicked and sweats were forming on her face. The boy- No, Naruto was going to be executed because of her. If only she had not rejected the boy, he would not have to die a meaningless death. No! He can't die! She won't let it happen! Mewtwo bit her lower lip and scowled. She had to do something! Anything! Frantically searching for a way out, a proverbial lightbulb lit atop her head.

That's it!

She had always maintain a force field that negate the electricity, preventing it from hurting her, but she never really deliberately put in any effort to retaliate. She just had to unleash all her powers to destroy the offensive machines. And destroy she did. Her eyes illuminated a violet effulgence as she channelled the unfathomable powers within her to crush everything around her.

The humans didn't know what hit them.

Memories- No! Nightmare of her years of horrendous abuse had allowed her to fuse her pent-up rage into her powers. Mewtwo growled in exasperation and fired an orb of nefarious energy at the control room. A devastation explosion split the facility apart and set everything ablaze. The rampant inferno was like a famine beast, devouring the area like a furious beast of fire. Mewtwo grinned with triumph and delight at the sweet cries of the hapless humans; they were writhing as the flames ate away their flesh.

"No! I don't have time for this! I will celebrate my victory later. I need to find Naruto!" Closing her eyes, she enhanced her sensing abilities to pinpoint her target's location. She sighed in relief when she found the boy, but she had to hurry before it's too late.

"Wait for me, Naruto! I'm coming!"

X.o.X.o.X.o.X.o.X.o.X.o.X

When Mewtwo had found the boy, she was infuriated beyond cognisant at the atrocity before her. Naruto was strapped on an operating table and was about to be injected with a lethal dose of poison. To her horror, the humans had intended to dissect the boy's body for further research! How depraved can humans be? In the midst of righteous fury, Mewtwo exacted divine judgment on those vicious humans.

No mercy for the wicked! She spared no one and made sure those damnable humans taste her wrath. Unbinding the unconscious boy, Mewtwo scooped him up into her embrace and let out an ear-piercing sonic shriek, dispersing the clouds of debris around them.

"We are leaving this place… forever!"

Utilising her immense telekinetic powers, Mewtwo raised her hand and launched a blast of powerful psychic force from her fingertips, demolishing the ceiling into smithereens in the process. Without hesitation, she soared into the sky with Naruto in her hands and a huge sonic boom trailed behind her feet.

"Let's find our home!"

X.o.X.o.X.o.X.o.X.o.X.o.X

If there was one thing Mewtwo did not anticipate, it was the dreadful storm. The wind didn't howl at them. It screamed at them with beastly roars. The rain was torrential and it fell mercilessly upon the duo. The angry sea beneath them was reacting violently; its black waves rose to enormous height, ready to swallow those that stood in its way. Mewtwo winced as a crack of lightning flashed through the blanket of ominous grey clouds.

Fatigue was overtaking her senses. She didn't know how long she had been flying in this unforgiving sky, but it was her sheer willpower that kept her going. "Just a little more and we can-"

A jagged bolt of lightning pierced her tail, much to her distress. She yelped as sharp pain coursed through her body, as if thousands of needles had simultaneous stung every part of her being. Her body went through a spasm frenzy before her consciousness started to fade away. Descending from her flight, Mewtwo could only mutter one word before darkness consumed her.

"Naruto…"

Mewtwo and Naruto pummelled and crashed into a nearby mountain, but their fall was cushioned by the gargantuan layer of snow. Their limp bodies tumbled down the steep slope like ragdolls. The swirling blizzard storm kept raging on, threatening to plunge the world in eternal snow. The impact of the fall and the sudden drop of temperature had woken the boy up.

"W-What happened?" Naruto flinched as the cold gale pricked his skin like torn and he struggled to open his eyes. Regaining his bearing from his disorientation, Naruto registered his vicinity. He was baffled to see an unconscious Mewtwo lying beside him.

All of his memories struck him at once. He remembered everything! He was restrained on the cold hard surface of a table, squirming and begging the scientists in a futile attempt to change their mind. They reassured him that his death would be painless. Suddenly, there were tremors in the facility that agitated the scientists. A-And… Mewtwo! He recalled Mewtwo barging into the chamber and raised hell on earth. It finally dawned on the boy what Mewtwo had done.

Mewtwo had saved him!

Crawling hastily towards his saviour, Naruto held the trembling frame of Mewtwo and whispered. "Y-You saved me!"

"C-Cold… So cold…"

The boy shook his head and brought Mewtwo's head closer to his chest. "I-It's gonna be alright! We're gonna get through this! Remember what I told you about my dream of exploring the world? Let's do it together! Let's go see the world with our own eyes! We finally escaped! We are not going to die on this day! You hear me? I believe we can overcome this obstacle! Don't give up on me yet! There are still many things we haven't done yet! I heard ice-cream tastes like heaven! We're gonna try it!"

"I-I'm sorry… I'm sorry for saying those-"

"It doesn't matter! We can get through this! I know-"

It was then they were disrupted by a faint outcry. Someone was calling out for them! Naruto turned his attention sharply to hazy mist and squint his eyes, trying to discern the flickering light from the distant sea. It was a shadow of a boat and it was heading their way. Naruto smiled in relief before he too collapsed to Mewtwo's side. The last thing he saw was a blurry image of a girl with golden hair yelling at him.

X.o.X.o.X.o.X.o.X.o.X.o.X
(Two days later…)

Naruto roused from his sleep and his eyelids flickered open. He caught a glimpse at the radiant sun peaking above the horizon outside the bedroom window. The dazzling ray gave him warmth, washing away his fatigue. Wait- Bedroom window? Naruto jolted up and his eyes surveyed the foreign environment warily. It was then the door opened, much to the boy's distress.

A girl, who was no older than twelve, walked into the room with a tray of food in her grasp. She pursed her lips in surprise when she saw the boy awoke. Skipping briskly to a table, she placed the tray down and beamed benignly at the confused boy. "Good morning, sleepyhead."

"W-Who are you?" A migraine struck him and he clutched his forehead. "W-Where am I?"

"You are in Celestic Town. My name is Cynthia Carolina. Nice to meet you." The blond girl concealed her giggled behind her sleeve. "My grandmother and I rescued you and your Pokemon two days ago. That storm was really bad. We were out fishing and didn't expect to encounter a storm of that calibre. You are very lucky."

Regaining his composure, Naruto managed to discern Cynthia's feature. She was really beautiful for a girl of her age. Her silky hair was pulled back into a pony-tail and her skin was pale as the moon. The beauty of eternal youth shone in her eyes. Those eyes carried such kindness. It actually frightened the blond to meet such an unearthly… thing. She was otherworldly! Breaking out of his trance, Naruto narrowed his eyes. "Where's Mewtwo?"

"Mewtwo?" Cynthia placed a hand on her chin and blinked. "I see. Are you referring to your Pokemon? My grandmother is a professor who has been researching the history of Pokemon for years. Even she didn't know what species your Pokemon was. We thought it could be some extinct Pokemon. Mewtwo, huh? Could it be a variant of the mystical Pokemon, Mew?"

Naruto simply arched a brow at the blond girl babbling to herself. She seemed to be aware of that and an embarrassed tint of red graced her cheeks. "U-Uh, sorry! I tend to do that. Anyway, I didn't catch your name."

"N-Naruto." The boy answered quietly.

"I see." A benevolent smile curled at her lips. "Your Pokemon is safe and sound. In fact, it is-"

"She." Naruto corrected.

"Ah." Cynthia would store that trinket of information for later use. "Do you want to see her? She is in the other room."

"Yes please!" The boy climbed out of the bed, but he didn't expect his legs to go numb on him. Losing his bearing, he felt himself tumbling to the floor. With dexterous reflex, Cynthia instinctively caught him, preventing him from falling. Naruto was flustered at how close the girl was at his face; he could practically feel her warm breath on his skin. "I-I'm fine. Sorry about that."

Cynthia chuckled and gave him the sweetest smile he had ever seen. "No sweat. Come on. Let's go see your Pokemon. I bet you're worried sick."

"Yeah… about that." Naruto slowly reached to his full height, albeit groggily. "Mewtwo isn't really my Pokemon. I… I'm just her friend."

The girl was perplexed, evident from her raised brow. "Doesn't that make you Mewtwo's master? Contrary to misconceptions, Pokemon isn't tool. They are our partners. Our friends. If she is your friend, then that makes her your Pokemon. And from the look of it, she saved you back then in the storm, didn't she?"

Naruto's eyes widened. Yes, he remembered. If it wasn't for Mewtwo, he would have died. "Yeah…"

"You wanna talk about it?" Cynthia softened her features. "It isn't normal for a kid like you to be wandering around in the place where my grandma and I found you. Not to mention, that area is isolated from civilisation. Tell me what happened."

An unnerving silence intruded. Naruto stared at the floor with a blank look. Not even a trace of emotion was reflected in his eyes. Cynthia resisted her urge to shudder at the boy's apathy. Scratching her scalp nervously, the blonde girl gave the boy a pat on his shoulder. "Don't worry about it. We can continue this conversation later. Let's go meet your friend, okay?"

"Yeah…"

X.o.X.o.X.o.X.o.X.o.X.o.X

"Who are you?" Mewtwo growled. She was no mood for games. Finally, freedom was within her reach. She could even taste it. But now she ended up in some strange place. She had every right to be hostile. God knows what misfortune or danger await her. Speaking of which, she had to quickly find Naruto. Unfortunately, she still hadn't recover from her injuries. If the area was well-fortified, she wouldn't have the confidence to say she could make it out alive.

"Do not be worry, young one. I am Professor Carolina. I am a humble researcher. Studying your kind has been a passion to me ever since I was a mere child." The elderly woman assured. She wore a sweater and a pair of khaki pants. Nothing extraordinary, except her lab coat. The lab coat that draped over her frail shoulders alarmed Mewtwo. And her eyes. Mewtwo was a good reader of human nature. She had to. Behind those sagacious eyes, Mewtwo could see something else. Something dark and dangerous. "If I wish to hurt you, you wouldn't be alive by now. So be a dear and drop your guard."

"What are you?" Mewtwo roared. "What do you want from me? Where's Naruto?"

The professor shook her head. "Lower your volume, fledgling. It's impolite to talk to your elders with such an abrasive attitude. Now calm down and-"

"I'm leaving!"

Carolina's eyes hardened. It was then Mewtwo understood. Those eyes belong to that of an apex predator. She felt a murderous aura choking her and paralyzing her body. The professor took a few steps forward, but Mewtwo had crawled back into the bed. "You can never leave this place until your wounds are heal. Because if you do, I will have to resort to drastic measures."

Mewtwo almost croaked. "W-What would that be?"

"Back before I was a researcher, I was in the navy. I was one of the best interrogator, actually. It was my job to come up with innovative ways to make my enemies submit. My point is… I may be a feeble human to you, but I had invented more than three hundred different ways of making man twice the size of me shit themselves." The professor smirked. "As I said before, I mean you no harm. But if you stubbornly refuse, I will have to tie you to a pole and force you to wear a helmet that clog your psychic reservoir."

Mewtwo swallowed her trepidation. This woman before her was telling how she would torture her with such a calm disposition.

"Of course you will start screaming. They always do. But no one will hear you. And then I will send hundreds of carnivorous Pokemon to your area. Your screams will attract their attention and stir their hunger. They will come to you. And you won't be able to run away when they come for you. They will feast upon your living body. You will feel every second of it as they tear you apart. You will die a meaningless death. Nobody will remember you. Nobody will know what happen to you. Or… you can just stay here and-"

Screw it! Mewtwo would not tolerate this nonsense any further. She was not about to let some homicidal old woman intimidate her. Mewtwo was about to channel her mystical powers when a sharp pain struck her. She collapsed like a puppet that had its strings cut and moaned.

"I told you to not to move around too much, didn't I?" Carolina rushed to the injured Mewtwo's aid, but her kind gesture was shrugged off crudely.

"Stay away from me!"

"Cease this foolishness. Your agitation is opening your wound. Look!"

Truth be told, the bandage tied around Mewtwo's tail was soaked red. Searing bursts pulsated around her throbbing wound, amplifying when her tail twitched. The horrendous pain was like a knife being twisted in her spine and every second of experiencing it was hell to her. Still, she had to preserve her pride; she was the strongest Pokemon for cry out loud. "I… I don't need your pity!"

The bedroom door swung open at that moment. Naruto and Cynthia barged into the commotion and were startled to see a very agitated Mewtwo glaring seething daggers at the visibly irritated professor. Deducing what had transpired, the blonde girl puffed her cheeks, placed a hand on her hip and pointed an accusing finger at her grandmother.

"Grandma!" Cynthia chided. "Did you use your 'I-am-from-the-navy' tactic again? How many times did I tell you not to do that? You will only scare people if you keep trying to scare the living hell out of them!"

Naruto ran towards Mewtwo, much to the professor's consternation. The Pokemon was still petrified and upset; it would be a bad idea approaching her. However, Carolina was shocked to see Mewtwo dropping her tension and apprehension in the boy's presence. Could it be that the bond between both the boy and his Pokemon had flourished to such extremity? The professor would unravel that mystery later.

"Old habits die hard." Carolina chuckled, but was fascinated that Mewtwo was being amiable to Naruto's touch. "Very well. I will leave you all to your device. Cynthia, be a dear and redo the bandage for the Pokemon. The ointment and the dressing are in the cabinet. Dinner at six."

The professor promptly ambled out of the room.

"I apologize on behalf of my grandma. She probably came on strong. If you know her well enough, you will know she is actually very nice." Cynthia let out a sheepish laugh and smiled weakly. "Yes, it is true she was once a navy officer, but that's history. Her tough exterior is just for show. Oh, by the way, my name is Cynthia. My grandma and I rescued the both of you two days ago."

Mewtwo ignored the girl's explanation and fixated her attention at Naruto. Caressing his cheek with her three-digit hand, the powerful psychic Pokemon nodded in relief. "I'm glad you're safe."

Naruto smiled. "It's all thanks to you, Mewtwo. Anyway, it's rude to ignore someone when they are talking to you. Mewtwo, be nice and greet Cynthia. A pleasant hello will do."

That only made the psychic Pokemon scowled and she grudgingly shifted her impassive sight to a bemused Cynthia. "Hm. I am Mewtwo. Thank you for saving us. I will repay you in due time."

"Ah." The blonde girl waved a dismissive hand at the Pokemon and walked casually towards the cabinet hung on the bedroom wall. "It's nothing, really. Haha. Here, let me patch you up."

When Cynthia approached Mewtwo with the medical kit, the psychic Pokemon was peeved and extremely vigilant, staring intently at the blonde girl as if drilling holes right into her skull. The fact that her eyes were glowing with malice wasn't helping either. If it wasn't for Naruto who let Mewtwo rest on his lap, Cynthia bet her arse she wouldn't be able to get ten feet near the paranoid Pokemon.

When Cynthia had clipped the last bandages together, Mewtwo's death glare of 'I'm going to chop your head off and gut you with a pitchfork' has lessened to a steady improvement of just 'I'm going to gut you'. In all honesty, Mewtwo actually liked the way the girl paid avid attention and care to her wounds. She might actually spare her life when the time comes for humanity's expurgation.

Mewtwo coughed uneasily and gave Cynthia a grateful nod. "Thank you."

The blonde girl giggled. "It's no biggie. Just all in a day's work. Come on, dinner's about to start. Let's go downstairs before my grandma yells like a navy officer. Trust me, you don't want to hear it."

X.o.X.o.X.o.X.o.X.o.X.o.X
Thanks for reading! I basically got this idea after watching that Pokemon Movie where Mewtwo speaks like a girl, then this random idea hit me.

Anyway, please let me know how you feel about this story!

As for Naruto's pairing,
1.) NarutoXCynthia
2.) NarutoXSabrina (This is honestly interesting, I really like her character)
3.) NarutoXClair
4.) NarutoXElesa
5.) NarutoXSkyla
6.) NarutoXHilda
7.) NarutoXDiantha
8.) Harem? (Is this even possible? I don't know. It depends, really.)

Please review!