Prologue:
The Sylph Company building is crawling with Team Rocket Grunts. Gym Leader and Team Rocket Boss Giovanni sits at the top of the building with the president of Sylph Co. discussing "business".
The Sylph Co. president, an elderly man, sits down uncomfortably. This intimidating man that stands before him controls the whole underworld of the Kanto Region.
"I feel that we must discuss what you're working on here," Giovanni says with a slight accent.
"I have no idea what you're talking about," The Sylph Co. president says worriedly. What could this terrible man want with his company?
"You know exactly what I want," Giovanni says menacingly staring the president down. "I want the Master Ball."
The Sylph Co. president almost faints. He has it in his pocket.
"I'm afraid that I can't let you have that," The president says, "That Pokéball represents years of scientific research and progression. I can't let it fall into the hands of some maniac!"
Giovanni smiles evilly and looks out the wall sized window overlooking Saffron City. Giovanni starts to laugh. Suddenly he pulls a gun on the president.
"I wish I could say that I'm sorry that I have to kill you," Giovanni says with no regret at all. "But I'm really not sorry." He shoots the president. The gunshot is heard throughout the building.
Giovanni digs through the dying man's coat and pulls out the Master Ball. It's a work of scientific art. He pockets it and then looks down at the dying man. He bends down to whisper in his ear.
"The Master Ball isn't for me," Giovanni whispers, "It is for something far greater than the Kanto Region or some silly science project."
As the Sylph Co. President leaves this life Giovanni whispers:
"HAIL HYDRA."