I loved the Mass Effect 3 fan explanation of the ending, tying together why Shepard saw the kid while fleeing Earth in the beginning, then again at the Catalyst while heavily wounded. Of the 3 choices, the red (destroying all the mass relays and the reapers) was the only one where he stopped limping to stand up again.

In Deus Ex Human Revolution, it's pretty easy to forget the opening cutscene by the time you're doing shit in China and get told to go to a clinic to fix your implants, in order to stop glitching. Said cutscene shows a bunch of shadowy figures planning how to control everyone with implants.

Grand Theft Auto and Red Dead Redemption 1 and 2 have tons of mystery easter eggs. Some of which have still not been 100% solved.

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.

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.

Control, in that the Board is really up to something that nobody can even begin to understand, and that the oldest house is not just a building on Earth that happens to connect to other realities and the astral world, but that Earth is actually one of those astral worlds...it's just held in place by the collective will of humanity.

It's something you miss unless you take the time to read deep into things.

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.

Inscryption. There was an ARG puzzle event at one point if you wanted to get REAL 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.

I was playing Cult of the Lamb and beating it, decided to look up any videos to see if I missed any lore or whatever, like what happens if you make other choices...

Surprisingly missed so fucking much about the world. Either the streamer was making up bullshit or the world is way deeper than I thought, with a whole history of why the crowns and gods exist.

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

Random weirdness that leads to wild speculation is always fun. Sometimes I'd like it to stay that way rather than an acknowledgement and a terrible semi-explanation.

Example : Anna from Fire Emblem. She's everywhere, on every continent, in every time period. She's often the generic item shopkeeper, sometimes she's in a relationship with some minor character... And sometimes she's managing your game's save data or hosting the tutorial, with absolutely no respect for the fourth wall.

It's weird, and it was more fun when it was never mentioned, like who or what is that girl, anyway?

Then Fire Emblem Awakening makes her playable, and basically, she's telling you. "Yeah, I travel through dimensions, and I have an infinity of identical sisters all called Anna. We're all traders, so sometimes we even compete for a specific market." There's a freaking side quest where you have to fight a bunch of Annas for this very reason.

Fire Emblem Warriors, following on that, has the multiple Annas used as a joke and makes her ubiquity the central trait of her whole character (in line with the very Awakening-like trend of making characters have one cringey character trait mentioned every second and absolutely nothing else to them).

I think it sucks.

Did you hear the one about what the bishop did to the horsey in chess?