The leader and founder of the Pokéxtinction organization is the notorious Mr. X, a scientist who was accidentally transformed into a Mewtwo by a nuclear reaction. Mr. X became evil, mad and power-hungry as a result of this transformation. Also with his transformation, he gained memories of the Great War between Pokémon and humans. His experiment accidentally created the Pokéumans, and he was determined to use them to become the most powerful being in the world.
At first, Mr. X used his genetic cloning experiments to create artificial humans to capture the Pokéumans. Later, he began brainwashing ordinary people to do the same. Brainwashed people are like sleeper-cell agents. They would live their ordinary lives. Once they see a human starting to transform, they will go into a trance-like state. Every brainwashed person will always say "You're one of them." Agents also carry a canister of purple gas with them, which can be used to instantly knock someone unconsious. Voluntary Pokéxtiction agents, who have a special technology to detect the transformation, will usually take the unconsicous Pokéuman and stow them in a truck and drive away. Any witnesses within half a mile shall have their memories erased by a special machine. Then, the Pokéxtinction organization will leave a clone of the person, who will live in place of the Pokéuman. Many clones don't realize they are clones.
Just like the Pokéumans, the Pokéxtinction organization also has secret bases hidden around the world. Voluntary Pokéxtinction members transfer captured Pokéumans in large trucks, usually a delivery or a moving van to Pokéxtinction bases. Most of the time, the Pokeuman Rescue Troop intervenes and frees Pokéumans from containment. But, if they fail to rescue a Pokéuman, they are taken to a Pokéxtinction base. Using Mr. X's technology, these bases are invisible to radar and human sight. Even so, there are many booby traps surrounding them.
A Pokéxtinction base is almost like a Pokéuman base, with dorm rooms, classes and a headmaster/mistress except that they are in factory-style buildings. Pokéumans captured will go to school like at a Pokéuman base except they will be conditioned to side with Mr. X. The classes also slowly brainwash them, and will become mindless puppets in approximately 5 months. Anyone who misbehaves more than three times, discovers a secret they weren't meant to, or goes against Mr. X, will have their mind instantly wiped. The bases also are full of rooms where evil experiments and machines are used. Mr. X travels to each of these bases once every two weeks.