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Why don't the police just show up to Team Rocket's headquarters with guns and arrest them and/or shoot them if they don't surrender?
Actually pretty much every plot of every Pokemon game revolving around these evil organizations trying to take over/destroy the world could be almost instantly solved by SWAT teams showing up to the organizations' HQs and terminating them. Why doesn't the player character or literally anyone involved in the plot ever do the responsible thing and inform the authorities when the lives of everyone in the region or the world are at risk?