Prologue:
Giovanni smirked. In front of him were rows and rows of Pokémon, strange Pokémon with abnormal features. Next to Giovanni stood a blonde-haired scientist with a lab coat and a blonde mustache.
"You've succeeded beyond my wildest dreams, Russell." Giovanni said, walking down the rows and surveying the Pokémon, who were in large glass cages.
"Most of them aren't…well…functional. Most rejected the DNA…they destroy themselves." Russell admitted quietly. Giovanni fixed him with a fierce look.
"What do you mean? Are there any that I can use?" Giovanni exclaimed furiously, wheeling on the scientist, who cringed.
"Y-Yes…six are stable. Here, they're in their own special room." Russell said hurriedly, leading his boss to a door at the end of the rows and typing in a code on a keypad to unlock it. Inside were five cages, each held a different Pokémon. One featured a red Luxray with his tail on fire, one a Lucario with apparent robot parts, one a Charmeleon with a blue mask not unlike a Monferno's, one featured a Dewott with wings, and the last was the most contorted of all: a Kadabra with a Scyther arm, horns on the back of his head, and a pair of green insect wings protruding from his back.
"They're…magnificent." Giovanni said, running his hand along the glass of the Kadabra's cage. "What did you do to them?"
"The Charmeleon is the most stable. We took DNA from a Monferno to give him the fighting type. He's faster and more agile than any Chameleon could hope to be, and much stronger than any Charizard ever can be. However, due to his cross with a fighting type, he can never evolve.
"This Luxray we crossed with a Pyroar. He's mostly stable, but he sometimes loses control of his fire abilities.
"This Lucario is my pride and joy. His right arm, both of his legs, one ear and one eye are all bionic. His legs are equipped with the same stuff that allows an Abra to levitate, so he can fly and hover. He is incredibly strong and fast. His eye can see through walls and zoom in on objects if he so desires. His ear can hear ten times better than a normal Lucario's. One unfortunate side effect is that with all the tampering we did to implant his bionics, he's mute.
"This Dewott we mixed with a Staraptor to give her wings. She's part flying type now.
"This Kadabra…well…this is the most twisted experiment we've done thus far." Giovanni's face twisted into a cruel grin,
"Well? What can it do?"
"He has a Scyther arm, as you can see. He can fly and still retains most of his psychic abilities, and he's also now part bug. His mind, however, is a bit…twisted. He's prone to violent mood swings."
"These are five. Is the last one…" Giovanni trailed off. Russell smirked and led him to yet another door in the back of a room. This security was much tighter, it involved a fingerprint and retina scan as well as a password. Russell pushed open the door.
Inside was a white cat-like Pokémon with a purple tail. He was in a test tube filled with orange liquid, and wires were connected all over his body. Scientists were everywhere in the room, monitoring the Pokémon via several high-tech machines.
"Mewtwo." Russell whispered in reverence. The scientist grimaced. "He came with a price, but…his vitals are much more stable than our other tries…and he isn't…deformed." Russell gestured to a smaller cage in the corner of the room that contained what appeared to be a pinkish purple blob.
"We call this one Ditto, after its ability to change its form into any Pokémon it sees. Has trouble with the face, though. The small blob turned around to face the scientist. Suddenly it began to change, growing taller and more humanoid until it was an exact copy of Giovanni…except for its simple two-dots-and-a-line face.
"Hmm. Might be useful." Giovanni grunted. Russell sighed,
"Good…we have dozen of them…and they keep randomly splitting in two to create more of themselves. Anyway, meet Mewtwo."
Giovanni turned his attention back to the feline humanoid.
"How powerful is it?" He asked the scientist. Russell just smirked.
"More powerful than any Pokémon alive, when it can control its powers." Giovanni smiled, then chucked.
"Perfect. No one alive can stop me now." He said. Russell smiled back at him. "Well, Russell. I take my leave. Congratulations; you've outdone yourself." Giovanni held out a hand, and Russell took it. Giovanni turned and walked out the door, Russell heaved a sigh of relief and stared at Mewtwo.
"You've pleased him. Thank you." Russell touched the capsule.
Suddenly an alarm filled the room. Scientists scrambled around, checking the machines in a panic.
"What's happening? What's wrong!?" Russell shouted, running to a machine and checking Mewtwo's monitor.
"He's waking." One of the scientists screamed.
"That's impossible! The serum should incapacitate him!" Russell yelled back.
"He's become too powerful!" Another scientist said before bolting out the door. Mewtwo awoke and broke from his tube in a blast of energy. Many more scientists followed. A containment machine went towards Mewtwo, wrapping him with wires and powerful mechanical arms. Russell sighed, the Pokémon was subdued.
He stood up cautiously. Blue light streamed through the gaps in the machine, and the containment machine broke apart, revealing Mewtwo. His eyes were solid blue; glowing with energy.
Russell scurried backwards hitting a wall and sinking down, cringing with fear.
"We dreamed of creating the most powerful Pokémon…" Russell said. The Mewtwo prepared to fire, blue energy gathering in its palm. "…and we succeeded." The Mewtwo fired, and Russell's world went black.
The Mewtwo huffed at the broken body of the scientist.
"Good riddance." He sniffed. He blew open the door and walked through. He spotted five genetic mutations, Pokémon like him, trapped in cages.
"Poor creatures! Those humans…they did this. I'll kill them all! And I'll put these poor, pitiful Pokémon out of their misery." He raised his hand.
"Wait!" The Charmeleon mutt shouted. The Mewtwo halted, staring at the Pokémon in confusion.
"Are you sentient?" He asked.
"Yes!" The Dewott mutt said. The Mewtwo paused.
"We want to live. We're the only sentient beings left in this place…just…let us out…please?" The Charmeleon begged. The Mewtwo lowered his hand and nodded.
"Very well. Get in the corners of your cages." He said. With five well-aimed blasts, he put hole through the thick plexiglass. The five Pokémon escaped.
"Thanks!" The Charmeleon smirked as he fled. The Mewtwo nodded.
He gave them ample time to escape, then looked down at his hands. Blue energy filled him and a blue light filled his eyes.
"Time for this human rubble to burn!" He released his energy.