Day breaks over the Eterna Forest, bringing with it the sounds and scents of life. Lush greenery surrounds Mewtwo and Mia and sweet aromas from the blooming flowers waft through the air. Mewtwo opens his eyes and sees the life of the Eterna Forest. He wishes for the peace to never end.
"Good morning, Mewtwo." Mia says, as she stretches and yawns. The sight brings a smile to Mewtwo's face.
"Good morning, Mia."
She smiles back at him.
"You know, you've changed these past few weeks." She tells him.
"I have? How so?"
"I don't know. It's a subtle change." She thinks about how to phrase her thoughts. "Hmm, I can't quite explain it, but you seem calmer; more at peace. Do you feel that way?"
"I've never thought about it, but I suppose I am."
She smiles at him one more time then sets off.
"Well, don't we have things to do today? Let's go!"
She leads the way out of the forest and Mewtwo follows suit. Perhaps this is what happiness is.
As soon as they leave the boundary of the trees, Mewtwo instantly feels something wrong.
"Mia, stop!" he almost shouts, causing her to jump.
"What's wrong?"
"We're being watched. Someone has found us."
Before he can sense anything happening, a flash of red tentacles whips Mewtwo with crushing force, sending him flying backward.
"Mewtwo!" Mia screams with shock.
Their attacker descends from the sky slowly. It stares at them with cold, hard eyes. Mewtwo stands up and recovers from the attack, but he feels a slight bit of fear as he sees what it is.
Inside the Hall of Origin, Arceus continues to watch over the world. He ponders the world that he created. He contemplates the life that thrives in that world. A rage builds inside of him. Living in his world are creatures that were never supposed to exist. They are abominations; they are imperfections in his perfect world. They must be destroyed! Arceus remembers the final days of the war against the humans. They were down to their last trump card; a pokemon that they created by accident by exposing a space-borne virus to a laser. This pokemon that they called Deoxys was supremely powerful, stronger than most of the Ageless. Arceus himself had to battle this creature and ultimately, Deoxys was destroyed. At least, that is what the rest of the world was led to believe…
Outside the Eterna Forest, Mewtwo and Mia look up and see the form of a new enemy. Deoxys, the DNA pokemon, returns their stare. It has come for Mewtwo.
Mewtwo has heard of Deoxys; stories from the Ageless and normal pokemon alike. He knows that Deoxys is strong and he knows that this time, there is no running away.
"Mia, go hide." Mewtwo tells his companion as calmly as he can.
"What is that thing?" Mia asks in fear.
"It is called Deoxys and it is here for me."
"Is it another Ageless pokemon?"
"No. Deoxys was an accident, created by humans, but its power matches that of the Ageless. I thought that Deoxys was destroyed by Arceus long ago, but it seems I was mistaken."
Mewtwo does not take his eyes off of Deoxys for even a split second. He cannot believe that the Ageless would resort to sending Deoxys after him. This time, they've gone too far.
"Hide, Mia! Quickly!" Mewtwo orders her.
In an instant, Mewtwo leaps forward attacking Deoxys with his Psychic power, but it seems that Deoxys is faster, changing into its Defense Forme and shrugging off the assault.
What?!
The virus pokemon morphs into its Attack Forme and fires off its strongest technique, Psycho Boost. The mass of psychic energy crashes into Mewtwo and slams him into the ground. He has never felt pain such as this before.
This is not like anything I have ever faced before. Deoxys is far stronger than I am.
Mewtwo stands again, but this time his body takes longer to recover. Deoxys continues staring down at his enemy from its elevated position. It has returned to its Normal Forme.
"So you really mean to kill me?" Mewtwo asks the virus pokemon. "Tell me, who sent you?"
Deoxys does not respond. Instead, it quickly shifts into its Speed Forme and rams into Mewtwo's body with Extreme Speed. The impact instantly knocks the wind out of Mewtwo's lungs and sends him crashing back into the forest, leveling several trees along the way. Mia comes running to his side.
"Mewtwo, are you okay?!" she says in a panic.
"I'll be fine, Mia. Now quickly get away from here! This place is dangerous!" Mewtwo orders her.
Before he can even stand this time, Deoxys shifts into its Attack Forme and uses its tentacles to grab Mewtwo by the throat. The virus pokemon picks Mewtwo off the floor and begins to choke the life out of him. Mewtwo's battle instincts kick in and he quickly summons a barrier that pushes Deoxys back, freeing Mewtwo from its grip. With room to move, Mewtwo launches a counterattack, firing an Aura Sphere straight at the virus, but once again, Deoxys reacts by switching to its Defense Forme.
I won't be able to win this way. Deoxys keeps switching forms to adapt to my strategies.
Deoxys goes into its Speed Forme and crashes into Mewtwo's barrier. The barrier cracks, but holds. Deoxys continues ramming the barrier in order to break it while Mewtwo quickly tries to think of a new strategy.
I must strike as soon as it gets close. I will only get one chance at this.
As Deoxys returns for another assault, Mewtwo purposely lowers his barrier, allowing Deoxys to get close. Once it is within range, Mewtwo creates a blade of psychic energy and uses his Psycho Cut attack. Deoxys cannot avoid the attack so it shifts the position of its body to protect its central core, the source of its power, but in the process it loses its left arm to Mewtwo's Psycho Cut.
"I've got you now!" Mewtwo shouts.
He charges in for a finishing blow, but much to his horror, Deoxys quickly regenerates its damaged body and slams Mewtwo into the ground with its powerful tentacles. Deoxys stares at Mewtwo with its emotionless eyes. All it knows is destruction and right now, Mewtwo is its target.
"This is the way it's going to be?" Mewtwo says weakly. "So be it. Come at me with everything you've got."
Deoxys rises to Mewtwo's challenge and gathers energy for its most destructive Psycho Boost. It shifts into its Attack Forme to makes its final assault all the more deadly. The two fighters look at each other one more time before Deoxys fires off its attack. Mewtwo readies himself, but before the attack makes contact, Mia jumps in the way.
"Mia! Get out of the way!" Mewtwo screams at her. He cannot believe what happens next.
A flash of light followed by an earth-shattering shockwave.
Mia's lifeless body is flung through the air like a wayward leaf caught in a windstorm. Time seems to slow down as Mewtwo looks up at Deoxys. He gathers the remains of his psychic energy and leaps forward in a wrath-filled frenzy. In its last moments, the alien pokemon, Deoxys, gives off a sharp and piercing cry. It does not even have time to feel the pain as Mewtwo rips it apart from the inside out.
Arceus finishes observing the battle between Mewtwo and Deoxys. The whole affair has left it feeling uneasy. The Creator leaves the Hall to ponder the future course of the world.
Mewtwo gasps for breath as he has exhausted most of his power to destroy Deoxys, however, he fights the pain in his body and walks over to Mia.
"Mia! No!"
He finds her lying face down in the dirt. As gently and as tenderly as he can, he turns her around so that he can see her face.
"Mia. Please, wake up." he begs.
Mewtwo looks at her, expecting some kind of response; a slight cough; a weak shiver; anything. He continues to wait, but nothing happens. He knows that she is gone.
"Mia. I'm sorry. I'm so sorry."
He feels his heart breaking. He wants to cry, but knows that he is physically unable to. He was created to fight, not to mourn.
"Mia did nothing wrong. She did nothing to deserve this. So then, why? Why did she have to die? WHY DID SHE HAVE TO DIE?!"
Mewtwo curses the Ageless. Their rules and their laws did this. He is their target, not Mia. Mia had nothing to do with this, and yet she was the one to lose her life.
Mewtwo picks up her lifeless body and carries her into the Eterna Forest. He can feel the warmth leaving her body. With his power returning, he excavates a patch of dirt and gently places her inside.
"Mia, thank you for everything."
He wants to say more, but cannot stand the thought of staying any longer. He pushes the pain away and focuses his rage at the Ageless. They are going to pay for this.
He shuts his eyes and in a flash of light, he vanishes from the Eterna Forest and teleports to Lake Acuity in the northern region of Sinnoh and waiting at the edge of the lake is the guardian of knowledge, Uxie.