~Three Months Later~

Red walked through the Rocket Hideout.  He had come back to get information on the missing eighth Gym leader.  Everyone who seemed to know something smirked and told him to go to Giovanni.  The young trainer finally walked to the elevator that lead to Giovanni's private study.

"Mr. Giovanni?"

"Admin, come in.  I assume you are here because you are looking for information about the eighth Gym Leader?"

"Yes, Sir."

"Look no further, I am the eighth Gym Leader."

"So, to collect all eight badges I must defeat you?"

"Oh, no, I know you are capable of defeating my Gym team, so, partially because of your loyalty, I give you my Gym Badge."

"Thank you, Sir."

"If you can defeat the Pokemon League, well, that would be most beneficial to Team Rocket."

"Of course, however, I feel that I should train my team further first."

"Logical approach, has that last Pokemon of yours evolved yet?"

"Machoke, yes, he is a Machamp."

"You plan on defeating the entire Pokemon League with just five Pokemon, leaving your sixth slot unfilled?"

"I have yet to find a suitable Pokemon to fill that slot."

"Well, I wish you luck."

"Thank you, Sir."

Red then left the base and released Charlie.

"To the top of Mount Silver, there we can train to be tougher than the toughies and smarter than the smarties."

~One Year Later~

Red stood at the entrance to the Pokemon League.  He smirked, for the Team Rocket Admin knew that his team was far superior to those inside.

~~~~+~~~~

"Charlie, finish this clown off with Air Slash."

Charlie sliced his wing through the air, creating a cutting edge that flew into Lance's Dragonite.  The Dragon type went flying into the wall and then unconscious.

"You have beaten me, and are now the Champion.  Or, you would be, but someone else has already beaten the Elite Four, meaning you must defeat them as well."

"No problem, Charlie here just defeated every last one of you."

Red confidently walked through the door to the Champion's room, to find Blue Oak standing across from him.

"Red!  You filthy Rocket member!  Today I will defeat you before locking you away in prison."

"No, today is the first day of my rule over Kanto."

Blue sent everything he had against Red, who used Sandy to demolish most of his team before she fainted.  Red then used Georgia to finish off Blue.  The grandson of Professor Oak had put forth his best, but was crushed by the Mount Silver trained Pokemon.

"I win Blue, today begins a new era."

"The politicians still have their powers."

"Not for long."

"Blue!  I came to congratulate you, but by the time I got here you have already lost to Red.  I am so proud of you Red!"  Professor Oak stated as he walked in.

"Glad to see you are proud of my strongest Admin."

"Giovanni."

"Samuel Oak."

"What are you doing here?"

"I came to congratulate my Admin."

"Blue?"

"Red."

"Red!  What, but he."

"Shut it old man!" Red and Giovanni both said at the same time.

"Red, you go on to the Hall of Fame and take care of that, Team Rocket is currently in an operation to capture everyone present."

"Yes, Sir."

Red went, by himself, and registered as Champion in the Hall of Fame.  The new Champion then returned.  The Oaks were missing, and Giovanni was standing with the other Rocket Admins.

"Red, we have one more mission for you."

"Sir?"

"A powerful Pokemon we created escaped.  We need you to capture it.  We will wait outside its lair while you go inside, and then wait for you to come out."

"Yes, Sir!"

"Meanwhile, our grunts will be executing our plan to make you the sole leader of Kanto."

"Yes, Sir."

"You of course, will answer to me."

"Why of course, Sir."

"Then come, a helicopter is waiting to take us to the beast's lair."

"Yes, Sir."

~Cerulean City~

 Red stood stock still, staring into the black abyss of the Cerulean Cave.  The Rocket Admin could feel pure power radiating from the cave.

"Red, this is the special Pokeball I told you about."

"The Masterball."

"That is correct. Remember, Mewtwo is extremely dangerous and will have no qualms about killing you."

"Yes, Sir."

Red then entered the cave.  He looked at the strange purple blobs that slipped throughout the cave, Ditto.  The Team Rocket Admin released Charlie for a light source.  Red traveled deep into the damp cave.

'Why have you come here human?'

"I come to challenge you!"

'Why?  I would win.'

"Would you?"

'Such courage, an excellent trait.  However, at this point it is stupidity.  The line between bravery and stupidity is so thin, that you do not realize that you have crossed it, until you are dead.'

"I am far from stupid.  I, Red, am the strongest trainer in all of Kanto."

'Yet, you work for that wretched man, Giovanni.  I sense, however, that you are not loyal.'

"I am simply waiting for a chance to strike revenge against him, he murdered my mother."

'And, I am a part of this?'

"You hate him as well, I can feel it.  I know it."

'You do not guard your brain well.  I can see everything.  You killed a Pokemon, yet you also try to be fair but strict.  You care about your Pokemon, but why?  You do not seem to mind killing others' Pokemon.'

"I do mind it, I avoid that situation whenever possible.  However, you avoided my question."

'Very well, I shall join you as your Pokemon, if and only if, you can best me in battle, not using that Masterball.'

"I gladly accept."

Mewtwo finally showed himself, floating down from the ceiling.  The Psychic type then levitated Charlie into the air, but, just before he could throw the Charizard, Mewtwo was engulfed in flame.

'Impressive, but will it be enough?'

Mewtwo then tossed Charlie into the wall of the cave.  The Charizard grunted loudly as he made contact.  The Fire type wasted no time though, and jetted flames at his opponent.  Mewtwo then used his Psychic powers to keep the fire at bay.  However, Charlie did not let up, and slowly, Mewtwo slipped and the Flamethrower hit him.

The Psychic type quickly countered by blasting Charlie with a wave of Psychic energy.  The Charizard stood against it for just a moment, before crumpling to the floor.  Red then released Georgia, who launched herself forward, clamping her jaws around Mewtwo in a Crunch attack.  The Psychic type flinched in pain before using all its Psychic energy to slowly pry the Gyarados's jaws open.

Georgia suddenly released a Hydro Pump pointblank into Mewtwo.  Caught off guard, the Psychic type went flying into the wall.

'Well done, Red.  Using my own weightlessness and concentration against me.'

Before Red could respond, Mewtwo blasted Georgia with a powerful beam of Psychic energy.  The Gyarados slipped unconscious.  The Rocket Admin then sent Sandy onto the field.  The Sandslash immediately took a speedy offensive, running around the cave and even across the ceiling.  Making it difficult for Mewtwo to land a hit, instead chipping away at the cave walls.

Sandy finally landed a Crush Claw onto Mewtwo.  The Psychic type took it as an opportunity to connect a Psybeam.  The Ground type flew across the room, and into the wall.  When the dust cleared, a small tunnel was revealed.  Sandy flew out of the wall behind Mewtwo, connecting a Dig attack before swiping with another Crush Claw.  Mewtwo had now registered what had happened and attacked, knocking Sandy unconscious with another wave of Psychic energy.

The trainer released Jasper, who summoned several Shadow Balls on command and launching a barrage of them at Mewtwo.  Only a few connected, but they did massive damage.  Mewtwo could not even keep itself in the air anymore.  

Red walked over to Mewtwo and touched a Dusk Ball to its head.  The black and green Pokeball variant whirred several times before clicking, signaling the capture of Mewtwo.  Red then released Mewtwo and his other Pokemon to heal them and detail his plan.

~~~~+~~~~

Red emerged from the cave to cheers from Team Rocket, unaware of what was about to take place.

"Red, you have done well.  Now, hand over Mewtwo," Giovanni ordered.

"No.  You killed my mother, and now, I take my revenge."

"So, you know.  You quietly gathered strength, waiting to strike.  Red, you think now is the time to strike, but really it is the worst.  Whether or not you hand me the Masterball, I control it and the Pokemon inside."

Giovanni pulled a small black remote from his pocket and clicked it.  The Masterball detached itself from Red's belt and fell open on the ground.

"What!  How can this be?"

"I am far from stupid Giovanni."

Red pulled the Dusk Ball containing Mewtwo out from his bag and released the powerful Pokemon.

'Hello, Giovanni.  I was once your pathetic test subject, but now I am the one ready to make you feel all that pain, and suffering.'

Mewtwo then used his Psychic powers to lift Giovanni by the throat, slowly choking him.  The Rocket Boss gasped for air and tried to reach his Pokeballs.  However, they had already been taken by Mewtwo.

'You are struggling for air.  Just like me when you tortured me for your studies!'

"Or my mother, when you beat her to death."

Red nodded to Mewtwo.  Everyone heard an audible crack as Mewtwo snapped Giovanni's neck and tossed his body in the river.

"I am the new leader of Team Rocket, and ruler of Kanto.  Anyone who defies me will perish."

Realizing that Red was more than their boss, that he was their king, all the Rockets got down on one knee and bowed their heads.  The king of Kanto, Red the Rocket walked over to one of the Admins.

"Did the other mission succeed?"

"Yes, all the high ranking officials have been assassinated."

"Good, good."

The new ruler of Kanto climbed onto the helicopter to finalize his new rule.