Just like real life, there are people who follow a left hand path and want to use the concepts of chaos and order to take free will away from the populous.
Ghetsis was a corrupt politician who took advantage of Unova citizens with legitimate causes and concerns and then he COINTELPRO'd (
https://en.wikipedia.org/wiki/COINTELPRO) the organization (or started the organization himself) into doing work for his cause while they believed their actions were for their own causes. You can even call the plot an allegory to the fight in modern day America for the first and second amendments (rights that were not originally guaranteed by the draft of the constitution that was signed.
I can not only distill the plot of BW and BW2, but I can also help anons understand it.
you all need to actually play these games not just speedrunkun thru the gyms. read what npcs say and talk to trainers post battle because they will say something new when you have beaten them.