Back inside his room, Dr. Wily II slowly walked towards his bed, and sat at the edge, his Pikachu still frozen in place in his hands.
You pesky RAT!! You almost blew my cover... I can't let you do that... Do you UNDERSTAND!?' Pikachu jumped out of Dr. Wily II's hands, and onto the bed, shouting and objecting to what his trainer had said.
"Pika!! Pi-pika-pi!! Pika-chu-pi!!"ENOUGH!! The old man is no longer around... Like they said... Out with the old... AND IN WITH THE NEW!!"Dr. Wily II raised Pikachu's PokeBall, and recalled it. Despite its protest, Pikachu was recalled, and the PokeBall shook violently.
"Oh no you don't." With inhuman strength, Dr. Wily II broke the release button mechanism on the PokeBall, preventing the Pikachu from popping out unless with external help. He then placed the still shaking PokeBall into the bed-side drawer, and locked it.
"Now with him out of the way... Time for some rest... AND PLOTTING!! MWAHAHAHAHAHAHAHAHAHA!!(I'm sorry... Pikachu...
)
(And time for a flashback to reveal why this is all happening...)
*****
Years before the Pokemon Mansion was destroyed, in an undisclosed location in said Mansion, Dr. Wily II was working on an Alakazam. This Alakazam was his life's work... His blood, sweat, tears... And it was nearing completion. Back then, Dr. Wily II was ambitious, total disregard for Pokemon life... This Alakazam... He caught it himself as an Abra, and trained it slowly until it evolved... All for this day.
The Alakazam had not been cooperative, why would it? However, his trainer wanted it to do follow his commands... How could it reject him? With puppy-dog eyes, the Alakazam resigned to its fate, as Dr. Wily II personally performed the lobotomy. As soon as the Alakazam's skull was opened, a massive surge of psychic energy hit Dr. Wily II squarely in the chest and head, causing him to fall to the floor. When Dr. Wily II finally woke up, the Alakazam's brain was already connected to multiple wires and probes. As Dr. Wily II looked at Alakazam's face, it was visibly crying. At that very moment, Dr. Wily II's ambitions, madness and memories they had together before this experiment were locked away, Alakazam's final wish for its trainer using that surge of psychic energy.... It used Disable.
*****
Present day, with the altered Alakazam completely incapicitated, the psychic lock placed on Dr. Wily II was released, causing his old personality to return. With a vengenece.