If you like pokemon and are willing to play fangames, Desolation has imo the best story of any I've played. The story focuses on Darkrai and I'm not going to spoil anything but it's got some interesting mystery elements involving him and his powers. It's relatively high difficulty though, not as hard as something like Rejuvenation or hacks like Rutile or Nova Sun, and not even close to any of the Kaizo hacks, but still on the higher end of fangame difficulty. It also has a cool mechanic called "field effects" which can be make or break for some people, it's kind of like weather effects or the terrains but heavily expanded upon and present in most battles. Like fighting in a forest buffs grass and bug type pokemon, fighting in a cave buffs rock type pokemon and makes using moves like earthquake too much cause a cave in that KO's all active pokemon, fighting on the water while surfing buffs water type pokemon and triggers water related abilities like swift swim, fighting in a desert causes all of the sandstorm related abilities to be activated, etc. I love that stuff, but a lot of people think it's too complex, especially people who don't play a lot of pokemon.
Ashen Frost is another excellent story driven fangame, and has a more approachable difficulty, but the writer insists upon undermining a lot of otherwise good scenes with jokes and references. He mostly keeps it to side content but it does creep into the main story sometimes, unfortunately. Still, it's what I recommend to basically anyone who's new to pokemon fangames since it's challenging but not too hard, and when it's taking itself seriously it's pretty well written. Ashen Frost's story is a noir inspired detective story, and it features some out-of-battle mechanics inspired by games like Ace Attorney where you need to piece together evidence to solve crimes, since the player character is a detective.