Author's Notes:

For Any Old Readers: Well, this is back. Years have gone by since my original foray into DNA, and I've come to realize the story I was writing, much as I loved it, was muddled and confusing. This is an attempt to revamp the story from the very beginning and flesh out the world that Ash and Mewtwo live in. This new beginning takes place towards the end of the Mewtwo Returns TV special. Up to Generation Four is pretty much canon. All the regions exist, but as to what part they will play shall remain a mystery for now.

For Any New Readers:This is an Alternate Universe take on the anime and particularly the movies up until Jewel of Life. In this setting, five years have passed since the Mewtwo Returns TV special, with some little changes and a bit shift toward the end: Mewtwo and his creations stay together instead of drifting apart. Ash, meanwhile, is a sixteen-year-old with the weight of the world on his shoulders and a deep connection to all Legendary and Mythical Pokemon themselves - whom I will refer to as The Divine for simplicity's sake. In this altered universe, things from the games and anime will be represented. All regions exist, but everything from Generation five and on - unless I deem it important enough - is not canon.

Warnings: Some swearing, uncomfortable moments and dark themes. I will try to keep things tasteful, but this is rated M for a reason, folks! It's gonna get gritty, raw, heavy and nasty. There is also an eventual pairing between Mewtwo and Ash, so keep that in mind before reading.

With all that out of the way, I hope you all enjoy this. I'm going to keep as much of the original as I can and refine things by removing the numerous time-skips. From here on out, my author's notes will be at the end - along with a list of the Cloned Pokemon, since they will be referenced a lot.

~Lady V~

Prologue: A Friendship Formed

For the first time in his short life, Mewtwo can truly appreciate what pain is and all the intricacies that come with it. The most noticeable and crippling are the jolts of white-hot agony that hit him when they move. Every slight breath or subtle jostle is enough to set off a new spasm that flares along his spine. Then are the dull thrums and throbs that are centered around his brain, and the sharp, brief stabs around his eyes that follow at the slightest hint of light. Lastly, there are the superficial stings from several shallow cuts and scrapes as a result of suddenly dropping to the ground.

The psychic-type smiles grimly at the observation for a moment, knowing that deep down his own curiosity was the only thing keeping concious through it all. Even as his lifeforce dwindled drastically, it seemed that his mind just wouldn't turn off. Was it a curse? A blessing? Hard to tell. Blearily, he looks over at his - what was the boy? Mentor? He briefly pictured Giovanni and shuddered. No, definitely not that! Companion? No. Ally? Maybe. Well, no matter the title afforded to the boy, Mewtwo found it fitting that the one who changed him through sacrifice would be the one to witness his final end.

There was no coming back from something as staggeringly final as this. It just didn't seem possible. So at the very least, he could at least die in the presence of someone who had shown him the light. For that reason, Mewtwo keeps on staring at him in spite of how hard it is for him to do so. He has but one final question.

Why? Why are you helping me? Projecting his mental voice causes a fresh flare of agony in his head. It takes every ounce of self-control to remain silent.

The boy seems to think for a moment before answering.

"Well, you saved my Pikachu. That's a good reason."

Though understandable, something about the answer leaves a bitter taste in his mouth. Perhaps that is what drives Mewtwo to continue the conversation.

The only one?

Instead of a simple nod or sign of confirmation, the boy continues to wear that same, confident smile he'd been wearing through their whole trek. The answer that follows is one that will stay with Mewtwo forever in it's sincere simplicity.

"Do you always need a reason to help somebody?"

Mewtwo thinks this over for a moment, recalling every instance in his life where this might apply. As always, Giovanni is the first to come to mind, his smirking visage sending a deep revulsion through him. Giovanni had been the first to offer a hand in friendship - no, in partnership. Though guarded and jaded at the time, something about the agreement had meant more than gaining power and domination over a world that seemed to harm him. At first, they had bonded quite well. There had been times he'd greatly enjoyed the older, more worldly human's company. Giovanni had been charismatic and charming at first, every word and action enthralling Mewtwo in ways that he'd never experienced before.

Yet over time, the dissonance between Giovanni's actions and words began to take it's toll on the seemingly powerful bond Mewtwo felt they shared. Promises were broken. Patience and gentleness became thinly veiled insults. Truth became lies. In time,it would be revealed that he was nothing more than a tool to the man who had become so much more than a business partner to him. A tool to be used, manipulated and contorted into the perfect slave.

He then thinks of the clones he'd selfishly created. He protected them and took care of them out of duty more than anything else. He was their creator, therefore he owed them. And in turn, they remained loyal to him - an army of cloned abominations just like him without a reason to fight. That's all they are to each other.

...

The thought makes him feel strange again, so he tries not to focus on that - his final thoughts should be peaceful.

Perhaps you are unique. A unique human. One of a kind.

The boy grins even wider as they move closer and closer to the exit. Light pours into the dark cavern, and through squinted eyes, Mewtwo can just make out the spring and the grassy meadow surrounding it.

"You're one of a kind, too. Everyone is."

He scoffs at that, slightly bitter. I don't know what I am, and soon, it may not matter. He screws his eyes shut against the light, the pain and weakness beginning to overcome his mind. They must have stepped out into the meadow, because the warmth of the sun's rays seem to dull a coldness that he hadn't realized was there. From there, things start to get a bit hazy. There are others talking to the boy, but the pain takes on a whole new level for him. Noise, sound, light, movement - all of it is a fresh layer of hell. Though too far trapped in his own agony to realize it, he lets out a soft mewl of pain, a show of weakness he would normally find inexcusable.

This seems to stop the talking, and the next thing he knows is the sharp coolness of water surrounding every inch of him. Along with that coolness, the pain begins to ebb away, slowly restoring his clarity and imparting him with very strange visions. And with this clarity and visions comes, as expected of him, thought.

Darkness. Thick, opaque darkness. The darkness does not remain long, however, as the vision shifts to an underwater view of sea grass flowing with a gentle ocean current.

I have seen that place. I have been there before. Was it in my dreams?

A pink creature with bright, blue eyes, looking at him in a friendly way. She darts off into the cloudless, azure sky, gone as quickly as she appears.

Mew?

The pain is quickly fading away now, his strength returning.

But this is no dream. I feel new life within me. If these waters have the same restoring effect an me as they do other Pokemon... Pokemon who belong to this world...

He sees fleeting visions of those he had cloned, hears their concerned cries as he gives himself to Giovanni...

...then he sees them in the past, marveling at the beauty of their first sunrise together on that mountain.

Could it be that I... no we... are not abominations after all? Is this world our rightful place after all?

Mewtwo opens his eyes as the last remainder of his pain and fatigue fade entirely. Smiling at this profound realization, he flies out from the water, chuckling in his moment of jubilation. This does not last long, however, as he is met with sudden explosions along the water's surface. Mewtwo shields himself and looks around as the smoke clears once more. Several helicopters come into view - all of them belonging to Team Rocket.

"They're here." Ash says grimly, as Bulbasaur and Chikorita stand by either side of him, ready to fight.

"Tell me where Mewtwo is!" Giovanni's angry voice demands over the loudspeakers. Several red orbs shoot out at him. He deflects them with his Barrier, sending them off to hit the ground without hurting anyone.

"Stop it!" An unfamiliar human yells boldly. "You can't come here and destroy the spring!"

Giovanni lets out a huff of loud, indignant air. "Yes I can! This place is mine!"

You will not defile this place, Giovanni! It does not belong to you - anymore than I do!

The sheer entitlement in the man's tone is simply too much to bare! No, it simply cannot be allowed! A sense of righteous anger courses through his veins as his psychic blue aura surrounds him once more. He begins to form a beam with that energy, considering killing the mob boss right then and there. But one look at his creations, who had come to offer whatever help they could give in spite of their vulnerability, changes his mind.

I'm not that monster anymore. He tells himself as he narrows the beam. I will not be what I was created for - a tool of domination and destruction!

This place has given me new life! I shall now use my power to defend it! Mewtwo declares for everyone to hear. He then uses the beam of psychic energy to destroy the crude devices that had been polluting the spring and any buildings the Rockets had been starting to make. He then uses his psychic energy to erase all of their memories and transport them to a far off island, far away from him, the mountain and his creations. He then sends the two scientists away, allowing them to keep a sample of the water. In their minds, he plants an inability to return or reveal his location. He does the same to the pink-haired human, the purple-haired human and their talking Meowth; though part of Team Rocket, he sensed a goodness in them. For that reason alone, he would not take their memory.

With those potential threats out of the way, Mewtwo smiles. There is an unfamiliar but very welcome lightness that floods through him. His power sings with harmony and contentedness. For the first time, there is no anger, no hatred, no feeling of inferiority to be masked by cold indifference. Saurtwo, Wigglytwo, Queentwo, Vultwo, Pikatwo, Meowtwo and so many others run to him. There are tears, there is laughter and cries of relief... and a very smothering hug from Queentwo. The psychic-type closes his eyes and relishes the moment, though it would confuse him later on.

It is alright, everyone. He reassures them gently. We are well.

Later that night, when everyone else has retired for the evening, Mewtwo remains very much awake. Flashes of the day's events flit across his mind in a jarring way, making sleep impossible. The psychic-type recalls all too clearly how close to death he had been, and that alone is enough to make him sick to his stomach. Shuddering slightly, he opts to leave the cavern to sit out by the spring. Sitting by the edge of the water, he looks up at the full moon and remains deep in thought.

Uncomfortable scenarios play in his mind; ones of what might have happened if he'd died or given in. Visions of his creations being forced to serve Team Rocket, or even being killed for sport are the most common. And thanks to his overly analytical mind, the mental imagery is far too graphic for his liking.

It's all my fault! I could have caused them to -

He lets out a very pathetic mewl at this, trembling as he tries so hard to remain strong. He curls in on himself, trying to blot it all out.

His creations laying on the ground, lifeless husks of who they once were...

Giovanni's cruel laugh as Mewtwo is taken away from his new home, his mind and body belonging to the evil mob boss...

Being made to kill his own creations, mindlessly obeying Giovanni...

Attacking Ash, whom he owed so very much, watching as the light faded from his eyes...

Suddenly, Mewtwo is brought out of his mental breakdown by the feel of a hand on his shoulder. He lets out a growl with his natural voice and readies an attack, only to stop when he sees that Ash is the one behind him. The boy, to his credit, doesn't even so much as flinch. Though clearly unnerved, there is no backing down. The psychic-type quickly pulls himself back together, disgusted with his display of weakness.

I apologize for that. He says coolly, taking a deep breath. My mind was on... less than savory topics.

Ash nods at that, not a single ounce of judgement in his gaze. Cautiously, Mewtwo probes the surface of his mind. When all he finds is a genuine concern, he relaxes slightly and stares out at the water once more.

"You've had a hard day." He says with far more understanding for a human child. "It's okay if you can't deal right away." He opts to sit by Mewtwo, sighing softly. "I've had a lot of close calls too... usually because Team Rocket is trying to take Pikachu from me."

Mewtwo nods, not really sure how to respond. All this is completely foreign territory for him.

What do you do when it gnaws away at you like this?

"I talk to a friend." Ash says softly. "Sometimes, it's Pikachu or Bulbasaur... sometimes it's Brock or Misty. Heh. Before I became a trainer, I used to run to mom with all my problems, and she'd find a way to make it better. When it gets to be too much, letting someone else in really helps, you know?"

No, I do not know. I do not have friends to confide in.

"What about the others?" Ash asks with a frown. "They really care about you, you know. Especially Pikatwo."

Mewtwo shakes his head, hating himself all over again. We are not friends. They remain with me because I protect them and provide for them. I cannot burden them with my own problems.

"So, you're like a parent to them?" Ash asks after a while, a bit confused.

Mewtwo contemplates the question for a moment. A parent? Like Queentwo and Rhytwo? I... suppose I am in a fashion.

"Well, uh, I guess I get where you're coming from. I know mom gets sad sometimes, but she never wants to tell me. Every time I ask, she always says it's her job to worry about me - not the other way around." The trainer's voice takes on a sad quality. "But at least she's got Professor Oak - they're always chatting about something."

The two stare out at the lake quietly, not really saying much for a time. Just when Mewtwo thinks the boy has fallen asleep, however, Ash says yet another thing that proves to be his undoing.

"You know, we could be friends. Then you could have someone to talk to."

Mewtwo's eyes widen slightly at that, an odd, fluttery feeling in his stomach. You want to be my friend?

Surely, he had misheard. The boy couldn't possibly intend that! But before he could even exercise his powers once more, he finds himself the target of a hug; something he'd seen Queentwo provide her children with once or twice. His muscles stiffen - a natural reflex for someone like him.

"Yeah, I do." Ash says with surprising gentleness for an eleven-year-old.

It is these words that chip away at the psychic-type's reservations somewhat. Slowly, his arms move to return the embrace and he smiles a little in spite of himself.

In that case, I accept your offer. Thank you.

They remain like that for a few moments before ending the hug. Mewtwo takes a deep breath, grateful that the boy doesn't seem to remember anything that happened during their last encounter. No one could smile so genuinely at their almost-killer.

"You're welcome, Mewtwo."

In the end, he decides not to burden Ash with most of his problems, but conversation seems a bit easier between them after that. They would talk all through the night, mostly about things of little importance.

And yet, for Mewtwo, the memory of it would forever be one that he always treasured.

I know this is short, but it felt like the right place to end things. I'm going to try to adhere to a bi-weekly schedule at minimum, but I may post more chapters than that depending on how things go. I'll do my best, everyone!

List of Cloned Pokemon:

Pikachutwo - Pikatwo

Meowthtwo - Meowtwo

Venusaurtwo - Saurtwo

Charizardtwo - Chartwo

Blastoisetwo - Blastwo

Squirtletwo - Squirttwo

Bulbasaurtwo - Bulbatwo

Gyaradostwo - Gyaratwo

Vulpixtwo - Vultwo

Ninetailstwo - Ninetwo

Vaporeontwo - Vaportwo

Scythertwo - Scytwo

Pidgeottwo - Pidgetwo

Wigglytufftwo - Wigglytwo

Dewgongtwo - Dewtwo

Sandslashtwo - Slashtwo

Rapidashtwo - Dashtwo

Tentacrueltwo - Tentwo

Psyducktwo - Psytwo

Golducktwo - Goltwo

Nidoqueentwo - Queentwo

Seadratwo - Dratwo

Rhyhorntwo - Rhytwo