Pokémon does have songs that I think fit that darker ambient vibe. Here is quick list that might help you get on track/inspo
Hall of Origin: Pokemon Pearl,Diamond
Deep within Team Galactic HQ: Pokemon Pearl,Diamond
Drought: Pokemon Alpha saphire,Omea Ruby
Deoxys Appears: Pokemon Fire Red, Leaf Green

and I'm sure there are more in any of the later generation games.