Thanks to kaizerkingkoopa for his help with this and the suggestion for the setting.
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X-Men x Male Mewtwo Reader:

Setting:
This is set in a universe that combines a lot of stuff from the X-Men series, mostly from the various animated shows.

Character designs, backstories and personality traits will be lifted from those and a few other sources with very little coming from the live action movies.

No Shade to those movies, I just prefer animation over live-action.

Plot:
We all know Mutants are a result of humans being born with the X-Gene.

The X-Gene grants humans with it various powers and abilities ranging from mundane to extraordinary.

This X-Gene originated many centuries ago from the original Mutant.

A being known as Mew.

Mew:

Yes, Mew was the first Mutant and she possesses immense Psychic powers, immortality and the ability to morph into anyone and anything and possesses every single power one can imagine.

Mew is even immune to the Phoenix Force itself and it will obey any order she gives it.

As the world grew and changed and more Mutants came to be, Mew decided to leave this dimension and now only comes in for occasional visits.

She'd spend her time helping others, collecting things she found and interesting and playing.

Thanks to her ability to transform and access to every Mutant power, it was easy for her to keep a low profile.

However, on one of her little trips she ended up coming face to face with Apocalypse.

Apocalypse:

Apocalypse was a powerful Mutant in his own right who had been traveling the world and convincing civilizations that he was a Deity which inspired many myths.

He found her while Mew was saving a little girl who was being attacked by a bear.

He saw her using a few of her powers and after teleporting the girl back home, Apocalypse approached the Genesis Mutant and demand she explain who she was.

Mew turned and despite his massive size and intimidating appearance, she had absolutely no fear upon looking up at the Mutant.

All she could say was:

"You are tall, that's so cool."

Before he could ask again, she teleported atop his shoulders inspecting his suit and said what he was wearing was remarkably advanced, especially for this time period.

She constantly teleported, inspecting what she could see and deduced that Apocalypse was a Mutant who had enhanced himself with Alien tech.

Shocked that she managed to figure him out so quickly, Apocalypse demanded an explanation.

Mew then introduced herself and asked if Apocalypse wanted to play.

He attempted to punch her only to effortlessly stop his fist and fling him into the air.

From there they both fought and Apocalypse for the first time ever, found himself hopelessly outclassed.

She was faster, stronger, smarter, more experienced and Apocalypse couldn't even land one strike on her.

To make matters worse, she treated their fight like a game.

"Missed me!"

"My turn!"

"This is fun."

Those were only a few things she said as she casually dodged, weaved and retaliated.

She was holding back a lot while Apocalypse was giving it his all.

It was humiliating and after their little "game" she said she'd need to go but hopes they'll meet again soon.

She then vanished leaving Apocalypse to stew in anger and frustration.

His pride was destroyed and he wanted revenge on this Mutant girl, but that would be impossible.

He could tell she was was far beyond him and there was no hope of matching her.

However, Apocalypse grinned when he noticed a small strand of her pink hair on the ground.

He may have had no hope of defeating her, but something of equal power and loyal to him could.

Apocalypse took her hair and brought it back to his base to begin manufacturing a clone with her DNA.

It would take centuries for the clone to be fully born but Apocalypse had time.

After many centuries, Apocalypse had finally done it, he had successfully cloned Mew.

However, this one had a few alterations.

He was Male and had any and all forms of empathy removed to make him a merciless fighter.

This clone was you.

You:

Apocalypse also made attempted to alter your mind to make you loyal and obedient.

However this did not work, due to you being a clone of Mew your Psychic powers would not allow your brain to be tampered with and you immediately woke up and broke yourself free form your pod.

Apocalypse, outraged by this as your creator ordered you to stand down.

You of course did not do that and began looking around.

While you were developing your consciousness developed quickly and you were able to observe and hear everything.

Apocalypse came back to his base to check up on you and kept ranting on about how he was constantly being defeated by the X-Men and how he'd eventually turn the tables with you.

You understood you were a clone of Mew, you understood you were to obey Apocalypse and destroy Mew for him along with the X-Men.

However, it didn't take long for you to come to a realization.

"Why should I obey someone inferior to me?"

If you were a clone of Mew and matched her in terms of power and Apocalypse lost to her, that meant you were stronger than Apocalypse.

What gave him the right to order you around?

You unleashed a powerful burst of psyonic energy and began destroying Apocalypse's base to send your creator a message.

He did not control you.

No one did.

Apocalypse attempted to battle you but was easily defeated forcing him to retreat and you went on with your rampage.

Once it was done you stood amongst the wreckage of Apocalypse's base, surrounded by flames.

Thanks to the fool, with your empathy gone you decided you'd succeed at what Apocalypse failed to do.

You would conquer the world and make Mutants the dominant species.

You rebuilt Apocalypse's base and made it your own where you begin researching ways to enhance your abilities further.

Over many years you traveled all across the world and recruited many more Mutants who were angry at the world and humanity.

Some notable recruits include.

Gina:
Codename: Gengar

Terry Argos:
Codename: Tyranitar

Simon Axil:
Codename: Garchomp

Amanda Viego:
Codename: Gardevoir

Aaron Stone:
Codename: Metagross

There are many more you recruited and eventually with them you unlocked a new Power.

A power known as Mega Evolution that would unlock a Mutant's true potential.

It temporarily transformed transformed all Mutants under it's affects into creatures of great power.

Mega Gengar:

Mega Tyranitar:

Mega Garchomp:

Mega Gardevoir:

Mega Metagross:

You in particular have gained the ability to switch between 2 Mega forms.

Your 2 Mega forms:

One form reduced your Psychic powers but upped your physical abilities to extremes and another weakened your body and made you more frail but boosted your already powerful Psychic abilities.

With these forms and your own team you were prepared to go to war against humanity.

However throughout your and gathering your team and resources you came across the group that gave your creator so much trouble, the X-men.

You encountered them multiple times under various circumstances and through them you begin doubting your plans.

Maybe this wasn't the best coarse of actions, maybe there was no need to start a war.

Will you change and finally learn compassion or will you rule the world with an iron fist.

We shall see.

Extra Notes:
In this story to go with your Mega Form Mew will also have her own Origin form when you and her finally meet.

Origin Mew:

Mega Evolution still causes pain to all who use it apart from you, they just fight through it here due to their devotion to you.

It will play a factor on your path to gaining compassion.

That is all.

Love Interests:

Rogue:

Storm:
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And here's my idea.

I just really wanted to use Mewtwo for something and this is the result.