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I'll start with Team Flare. They're pretty easy to '''improve.'''
>AZ cooperates with them out of revenge towards Xerneas/Yveltal, and pretty much becomes the N of X/Y.
>Lysandre wants to take over the energy industry of Kalos, so he sabotages the solar power plant and uses it to promote his new energy project.
>He develops Geosenge Town into a boom town that will oversee the ultimate weapon's conversion into a power plant.
>Around the middle of the story, the player will hear news about a dying forest/a wasteland coming back to life, disturbing the local ecosystem.
>If they go there, they will see a site guarded by Team Flare, and a crater/empty nest at its center.
>Upon visiting the poke ball factory, the player is ambushed and caught by Team Flare, forcing them to do an escape without Pokémon.
>After getting back your Pokémon and ridding the factory of Team Flare, the owner gives you a Master Ball as a reward
>At Team Flare's secret hq, it is revealed that Lysandre got a Master Ball from the factory to control Xerneas/Yveltal
>He explains how the legendary pokemon ignored the needs of others/caused harm to others and says that they need to pay the prices of their actions.
>Upon the power plant's activation, the lights of Luminose city-turned off for the activation ceremony gradually turn on as the legendary pokemon's agony worsens.
>Of course, AZ changes his views as he interacts with the player, betraying lysandre by breaking his Master Ball.
>He then fights alongside you against Lysandre's four mega Pokémon
>With the legendary pokemon freed, the power plant destabilizes and collapses, just like the actual games.
What evil teams will you people improve with your QUALITY writing skills?