Which games have real living worlds?

no fauna or flora become extinct

This is a thing in FFXI too, but the system is so complex that I think it'd be easier to hope that you remember it, than to try to explain it.

Sure, it's not 'absolutely permanent' (except that one time) because well, code for this is usually reversible or people desire it to be reset-able, but this one is on the Devs to intervene and do.

Well, looks like that's the end of them.

Everything else is covered either by one of the prior answers, is common enough that people probably have actually had the experience in some game (like the holiday thing, games definitely have holiday events that actually change the world, sometimes permanently), or end up being moreso a question of how a player chooses to interpret a specific game mechanic (for example, Adventuring Fellow in FFXI you can only call once per day because they're doing their own thing, or a complete change in NPC spawn type in Elite Dangerous because the players associated with a specific faction tend to do a particular type of mission more often, our Faction explicitly spawns extra Cruise ships and Personal Convoys because one of our largest subdivisions is Tourism and many of our players spend lots of time doing Passenger missions, we expect the game tracks this too).

So, thanks for the hour or so of fun, hope all enjoyed, we're done for now though.

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Pretty much the only reason we're here.

It's been changing away from that a lot, though, especially since Jeff left, so probably not anymore.

So it goes.