Not games with a convoluted mysterious story, per se, but if it’s something that re-contextualizes the story somehow, that’s the kind of thing I’m interested in.
Inspired by my digging into the FF:06:5B mystery in my current playthrough of Cyberpunk. There are all sorts of weird codes and ciphers, bizarre rituals you have to do at certain places and times, and vague clues in weird places. One clue was even in an update to The Witcher 3, apparently. Based on my reading, the community found a sort of conclusion to this one, but it really doesn’t clearly explain things (though it fairly strongly hints at Night City 2077 being a simulation, and us not really playing V, but rather whoever is breaching the system at the title screen).
There’s the fan theory from the Pokémon Black/White series that N, the half-rival/half-enemy, is secretly a Zoroark. He has a similar hairstyle and it would explain his backstory as a wild child and why he somehow has the ability to understand Pokémon. There’s also a chase sequence where you follow a Zoroark around, but you reach the dead end of a cave and it’s just him there.
Portal 2 has a big one that I think most people miss. You can find the biggest clue at the „bring your kid to work day“ exhibit where one submission of (I think it was) a potato plant was signed by a kid named „Chell“. Same name as the protagonist. It‘s easy to miss but it puts the entire story (many parts of which you can also miss) into a new perspective. I always loved that and was very surprised to her many players completely missed the connection there.
Inscryption. There was an ARG puzzle event at one point if you wanted to get REAL deep.
Didn’t that require months of community coordination to solve?
Something like that. I don’t know the details, I just read about it after I played the game. Something like that is far beyond my scope.
Yeah that thing was excessively deep.
Noita is full of these, being designed specifically to require community cooperation to solve, but the big unsolved one is the Eye Messages. They must be important, because they’re one of the only secrets that won’t appear at all with mods active, but nobody’s managed to decide them yet.
Blue Prince kind of fits. You can accomplish the stated purpose of the game, and even see the credits roll. But if you keep poking around afterwards you realize you’ve barely scratched the surface of mystery/story to uncover
