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I'm thinking something that brings it closer to the gameplay of mainline games, fanfic incoming
> Years after the events of Pokémon XD: Gale of Darkness the region of Orre has slowly changed.
> While still mostly arid, parts of the region have been revitalized due to climactic experiments carried out by the now expanded Pokémon HQ Lab in an effort to better diversify the region
> Previously discovered Poké Spots have grown over the years, becoming akin to Wild Areas and some new spots have been discovered along with the discoveries of some new Pokémon and Orre regional variants
> These changes and discoveries have created an influx of Humans and Wild Pokémon
>Changes to old settlements and the founding of several new settlements/establishment of routes
> Team Rainbow Rocket is back again and, interested in the use of Shadow Pokémon, have brought Cipher into their ranks
> In an effort to further prevent purification and push the technique, they have developed Spectral Pokémon
> These are essentially Shadow Pokémon but now with an extra (defensive only) typing and a new aura to match
> The technique is being tested on Pokémon brought from other regions, by villains brought from other worlds as well as those previously seen in Orre
> Each villain is based in or near the settlements, defeating them is the equivalent of defeating gym leaders to progress the story
> Michael is now the head of the Pokémon HQ Lab and tasks the protagonist with figuring out where and who these new Shadow-like Pokémon are coming from and capturing/purifying them
> Gifts the protag two Eevees
> New Dragon type Eevee evolution
> All Eevee evolutions get megas that add one of the typings not seen in Eevee evolutions (including Normal type)
> All/most trainer battles are double battles
> All other megas and regional variants return, these Pokémon are obtained as Spectral Pokémon
> Legendary Pokémon and Ultra Beasts obtainable in the endgame as Spectral Pokémon