This has always been my idea to change the Pokémon formula.
The game opens after a natural disaster in a new region. The storm has passed and people are beginning restoration. Towns are still rebuilding, many are without electricity, and generally the region is still in a calm state of complete disorder.
In the wake of the storm, the government sends supply and resource vehicles around the region, but people are still struggling. So the game's criminal team does so as well, delivering supplies and aid to regions and currying favor with the populace. Therefore the criminal organization is establishing their own infrastructure and gaining influence unopposed.
Instead of collecting badges, you travel from town to town on your way to your parents, who you were separated from while you attended school. In each town, you have to help the relief effort. Clearing avalanches, restoring power, delivering medicine, typical RPG stuff.
Game has a heavy emphasis on human relationships with nature as humans and Pokémon attempt to restore order to the region. Eventually a scientist says there is seismic activity that they are afraid is another tsunami, so you must battle and catch that legendary Pokémon. The gimmick of this legendary, as an unstoppable legendary force, is that no matter how good of a trainer you are, it doesn't always obey you.
The end of the base game is reuniting with your family, which causes a one year time-skip. The post-game is the actual traditional, badge-collecting game where you can now go to all the towns you helped and become a Pokémon champion. You must also now dismantle the criminal organization that has gained so much oppressive power in the region.
This was inspired by the Yakuza making donations and efforts in the wake of the most recent Japanese tsunami.
The game wouldn't be grimdark, or deal with death at all, it's hopeful and humble in tone.
I actually wrote a whole outline for this game on the old Nsider forums a million years ago. That's the Pokémon game I always wanted as a teenager.