The champion's love(Cynthia x male reader)

The shrouded mystery

It has been 2 weeks since the Y/n beat his girlfriend. They have currently decided to buy a house to live in together in the Sinnoh region. Y/n is still able to transfer from Kanto to Sinnoh  easily. Right now Cynthia is waking up in her bed and turns to greet her boyfriend but he isn't there. She walks down the steps and sees all of his pokemon are there which is strange.
Cynthia:Hey you guys where is Y/n?
The pokemon shrug signalling that they don't know where he is. All except charizard. He know exactly where his partner is.

We now see a cloaked man who has a keystone on his bracelet walking up to a building. He walks in, taking out the front guard of a door that has a faint R mark on it. His face is hidden so his identity is shrouded in mystery.

???:Here it is. One of Team rocket's many bases. Little by little I will end team rocket.
This figure has been taking out bases by bases with his team of pokemon. He enters the building and an alarm is instantly activated.
???:Figures. And now grunts should be swarming me in three. Two. One.
A horde of grunts come in the hallway and block off his path.
Grunts:Don't take another step.
They all send out their pokemon as the figure sighs.
???:And now I will obliterate you. Go!
He throws a pokeball and the pokemon that comes out shakes the grunts to their cores. It is a purplish pink bipedal pokemon that has a huge menacing look on his face.

Grunts:Take it out! Use Shadow ball/Poison sting/Sludge!
The raticates, Golbats and Weezings send their attacks.
???:Teleport.
Mewtwo vanishes into nothing and avoids the attacks. He then reappeared behind the pokemon.
Grunts:Behind you do it again!
???:Psystrike.
Mewtwo materializes an odd psychic wave to attack the targets. They all plop down to the floor instantly. The grunts are astonished and Mewtwo glares at them. They all pass out from fear.
???:Good work. Let's keep going.
The two of them keep walking through the building as they take out many grunts. Halfway through the building the man received a message from his earpiece.
Oak:Y/n I am getting a map of the the top floor. There seems to be about 100 grunts and one admin. Looks like it is Petrel.
Y/n:Thanks professor.
Y/n and Mewtwo burst through the door. The grunts and Petrel look ok in shock.
Petrel:An intruder. How the hell did you get this far. And how do you have Mewtwo?!
Y/n:Your forces are weak. That's for me to know. Give up and I promise this won't be painful.
Petrel:Fat chance. Grunts attack!
Y/n:Huh.I tried to do this the easy way but you left me with no choice.
He activates the keystone on his bracelet.
Y/n:Mewtwo you are the manifestation of the mistakes of team rocket. Unleash your fury and become the most powerful pokemon on the planet. Mega evolve!
The light from both the keystone and mega stone engulfed the entire room. When the grunts and Petrel uncover their eyes they see the horrifying sight. Mega mewtwo y is levitating off the ground looking down at them.

Y/n:Psystrike.
Mewtwo sends another wave of psychic powers that is much more powerful than the small dose he gave to the grunts. It engulfed the entire building and the building exploded. The people of Mahogany town are flabbergasted and see the source. All they see are the fainted and burnt bodies of all the grunts and Petrel. Their alive but barely. The authorities are called and they are taken into custody. Y/n is seen with Mewtwo.
Y/n:Another one down. Good work.
Mewtwo:Thank you for helping me.
Y/n:Hey it's a trainer's duty to help their pokemon. I would do this for as long as it takes.
Mewtwo:Thanks.
Y/n:Oak where is the nearest base to here?
Oak:In the basement of Goldenrod radio tower.
Y/n:Let's go.
They teleport away to stop more of teak rocket. In the sky we can see Johto champion Lance flying on top of his ace watching the cloaked Champion teleport away.
Lance:Who is that?