>>34827895There could be a large group of Pokémon that formerly belonged to trainers that were abusive towards them, and continuously attack human settlements as a petty form of revenge, with the attacks getting more and more severe until one of the towns/cities the player visits later on has been completely razed to the ground. They could be rendered uncatchable to the player due to still being tied to their Pokéballs that they might be hoarding at a hidden "base" of sorts. There could also be scenes in the game where the trainer Pokémon can be seen being rallied by the runaways while their trainers are away, taking their balls with them so that they can't be caught again.
It'd also be cool if you could choose to help them at the expense of more and more innocent people getting hurt in the ever-growing attacks. On the other hand you could stand against them to where prevailing means that they'll either be imprisoned, killed, or be returned to the very trainers they sought to escape from.