This time the focus is on the bad guys, having just beaten a young trainer Pikachu with his Rhydon, Giovanni puts on a friendly facade "That Iron Tail was an interesting strategy, how about you try again later?"
"I will," said the kid, he left for the Pokémon Center
Giovanni presses a secret button, revealing this is his next secret base "How is the cleanup going?"
Archer brings the report "Sir, Step 1: Remove all physical evidence you were present in the Game Corner is 100% complete."
"And?" Giovanni glares
"Um… Step 2: Have the two witnesses who actually saw your face, Red and Oak perish in "accidents" is…" Archer begins to sweat "0%… complete…" he sees the glare strengthen "Oak's Pokémon are quite perceptive, they're too good at protecting him. As for Red, his movement is too chaotic, he's either in major cities where we'd be seen or he's untraceable in his movements. He's either extremely careful with calculated moves beyond our understanding or extremely lucky with random movements…"
"Damn it!" Giovanni hit a wall "What's his game!?"
Ariana comes over "Honey, Silver is in the next room, it's not good for him to hear you this mad…" she says, while also not comforting Silver
"MAD!? I'd be MAD if the Elite Four burst through the door, defeated everyone at the base, and discovered my secret! But a child!? I'm FURIOUS!" Giovanni punches the wall again, this time putting a hole in it! "It's the greatest humiliation Team Rocket has ever faced!"
"I-if it helps… we have good news…" said Ariana "We have just received word of the whereabouts of MewTwo! It's hiding in Cerulean Cave! Officially, only Indigo League representatives like you are supposed to train there, but we believe you can secretly tunnel us in using Dugtrio."
"Then we're going…" Giovanni states
Later, in Cerulean Cave, all of Team Rocket fights MewTwo! The 4 Rocket Brothers, the 4 Rocket Sisters, countless Rocket Grunts, all 3 Executives, Etto who brought a single Elekid much to everyone's annoyance, Jessie, James, Meowth, Butch, Cassidy…
MewTwo crushed all of them without breaking a sweat! Giovanni tried to fight MewTwo himself! Dugtrio, Kangaskhan, Nidoqueen, Nidoking, Rhydon… all beat in one shot!
MewTwo entered Boss Rocket's mind, resurfacing painful memories!
A bug catcher… beaten down by every traveler through the forest. Some went as far as bullying him, taking his stuff and his money when they won! He caught more and more types of bug Pokémon, he trained against wild Rhyhorn, and soon enough, he crushed traveling trainers! He took their stuff, he took their money! He got to bully his bullies! He began to diversify, using more than bugs, catching the Rhyhorn! He began to lose battles again as he left the forest more, he tried using science to power his Pokémon!
He found special radio waves could evolve Pokémon or even control them, most scientists refused after seeing how it caused the Pokémon extreme pain, filling them with rage! But a few agreed, they had to… skirt around laws and ethics for funding, but they did it!
Small side effect: They retain their pre-evolution color if evolved this way, it'd be impossible to keep secret for many species of Pokémon…
He goes so far in pursuit of strength, he sends an army of trainers after Mew… then…
The memory was too painful, even MewTwo couldn't undo the mental block! Giovanni looked at Jessie, then at MewTwo! He had no Pokémon, nothing to weaken MewTwo with but… his body! He punches MeTwo! Next thing he knows…
He's in a hospital…. eventually he is released, and his Pokémon are still on life support… he reads a newspaper "Silph Co. Finishes Prototype Of World's Strongest Pokéball!"
He tells the others "Red and Oak know my secret, Team Rocket's only chance is this Master Ball project! Everyone with a secondary team, bring them! All of Team Rocket storm Siph Co. HQ!"