>>43644074A villain that is obsessed with control, for that extent, he wants to use whatever the box legendary is to control the destiny in all the universe and all randomness in nature for he thinks the inherent chaos in the nature is what makes people unhappy, and if people can make rational decisions that can't be affected by this randomness, everybody will achieve their dreams.
The villain will be hidden behind curtains while he controls proxy several thug groups (such as Team Skull) he brainwashed to think like him. These groups will try actively to brainwash other people in their cities, and wreck shit if they can't.
Few clues can lead you to the man pulling the strings, and stopping him will be completely optional. However if you do, you are revealed that he, in turn, was controlled by a legendary Pokémon, which through history has controlled nihilistic people to achive its ends.