Pokémon: Operation Kanto Sweep
I made some small edits to this chapter, such as appearances and names. Otherwise, it's the same thing, except for a few grammar edits.
The surgeon rose from the three bodies on gurneys, moving over to log yet another entry – his final concerning his patients. His fingers flew across the keypad, quickly typing his thoughts as he monitored the three's vitality out of the corner of his eye, watching the luminescent blue screen more out of habit than concern. Everything was perfect – he had seen to it himself. There would be no problems.
"They're ready," he typed, checking the door for activity: he would be expecting someone soon. "They are the most capable trainers the world has ever known. Agent Green will rise to the title of Pokémon League Champion – her success is without question. Agent Red and Agent Blue, however…" The surgeon stopped, turning to look at the still faces of his patients, green, red, and blue hair contrasting harshly with their monotonous uniforms. All three of them wore the silver and black of the Three Beasts' trainees. Adjusting his glasses, the surgeon turned back to the screen, quickly concluding his first log. "The boys have potential, but they haven't shown quite the cunning that Green has."
"Each agent will be provided a single Kanto-native Pokémon at the start of their journey and will be dropped in Pallet Town, cared for by two "mothers" that Team Rocket has arranged to act as such until further notice. Agent Green will set out on her journey a month ahead of the other two; this will allow her time enough for an uncontested victory in the Pokémon League, besting even the Elite Four."
"As for their Pokemon... Green will have that Bulbasaur she caught south of Victory Road, Blue will keep the Squirtle he found in Vermillion City, and Red will use the Charmander he stumbled upon in Viridian Forest. Surgeon's note: patients in full health, amnesia confirmed, no damage to either the body or mind since treatment. Assignment complete." He finished typing his final entry, and logged off of the system.
"Well done, Blaine," a voice said from behind the surgeon, the sliding door having already closed quietly behind the imposing figure. A Persian brushed against his legs as he walked over to the three comatose agents, resting a hand lightly on the side of Green's bed. "Well done indeed."
Blaine inclined his head respectfully, acknowledging the man's superiority. "Of course, sir. Their real memories are all but gone now. However, if they do not complete their missions within the coming year, Team Rocket will have to take measures to eliminate them, as you know well."
"You need not concern yourself with such things. I have contingency plans in motion." the man replied brusquely. "Your job with them is finished... for now. They will be fine."
"They are the most talented trainers that Team Rocket has recruited, after all," the surgeon agreed, shrugging passively. "However, with these false memories we gave them, it may be difficult to arrange the victor's ascension as the leader of Team Rocket…your successor may not agree to succeed you. Be careful, Giovanni."
'I know that…" Giovanni said quietly, clenching his jaw. "But it must be done."
"Sir, it's dangerous to remain here any longer, we must leave immediately," the surgeon cautioned, looking at his watch. "Time is up."
"Then send them to Pallet Town. I want them back as soon as possible," Giovanni declared, sweeping out of the room. "Prepare to leave. Next week you will commence Project Gemini."
Blaine worked quickly, unhooking each of the three agents from the machines that sustained their comatose states, carrying them individually to the helicopter that waited outside, careful to avoid everyone. As he placed each child in the helicopter, he placed a folder inside their vests and a bag with clothes beside each of them, slamming the door and waving to the helicopter to leave as he placed the final agent inside. As the helicopter disappeared into the low, pre-dawn clouds, he could hear footsteps and cursing coming from the operating room, lights flashing as he was discovered.
Far away from the secret laboratory, the helicopter landed at Pallet Town. Three agents arrived to bring the trainers to their new homes and "mothers". Six months later, the girl, accompanied by her Bulbasaur, set off on her journey without looking back. The Squirtle and Charmander were hidden away until the day of the other two's departure, one month after Green's.
Finally, it had begun.
I'm getting most of my information from the games FireRed and LeafGreen. The kids' uniforms look a bit like miniature versions of the Three Beasts' uniforms. Red's is like Orm's, Blue has Carr's, and Green customized her version of Sird's uniform, getting rid of the ridiculously long belt and sleeves.