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).
A few years ago I stumbled down a rabbit hole that led to the Shadow of the Colossus fan theory community.
If you play the game normally, you’ll wander a deserted, forbidden land and defeat the 16 colossi, revealing a little more back story each time, see the finale, and finish the game.
If you explore every nook and cranny of the world, make careful charts, compare the PS2 original and the re-releases, and even hack the game to take the camera out of bounds, you’ll find an astounding amount of detail that, at first, seems to be wasted. But over the years, fans have turned all of it into a surprisingly coherent possible expansion of the game’s universe, including linking it more directly to the developer’s previous game, Ico.
For a long time, many people were sure that some hidden secret remained buried in the game, to be revealed if only the right set of actions could be discovered. Most of the community seems to have given up on that now, but looking at what they assembled, it’s hard to shake the feeling that there still may be something to it all.
I loved that game. I still play it every few years.