So, in game design terms, there are actually some pretty straightforwards ways to add more serious end-game style challenges to open-world games. Not trivial to implement, but definitely do-able.
Generally speaking, a heavily open world game gives little story control over where major elements appear in a game. The equivalent of an end-game dungeon could be placed in the far corner of the game world, or it could be a block away from where you start. You can write routines to moderate that placement to some degree, but you can’t have TOO many restrictions, or it becomes a designed world rather than an open one. In any case, placement and world constraint can’t really moderate the player’s access to end-game scenarios and content in an open world game.
However - player activity and skills CAN. If I have certain key player actions trigger major changes to the game world, or open access to late game areas that are otherwise sealed off, then I can create stepped challenges in the game. Terraria does a great job of this, while still retaining a fairly ‘open-world’ feel to it.
In this methodology, most serious story elements, later dungeons, bosses or end-game puzzle rooms are tightly sealed within local complexes (like a sealed lab or vault), and/or summoned by player actions. Say, by setting up a specially coded transponder at any radio station tower, after hacking the special transponder codes out of a basic lab’s computer system, or something.
Usually this results in a couple things happening. Maybe a boss or a major story NPC shows up shortly after the player does the thing - and perhaps one or more major parameters of the world change, often with the end result of making the place more dangerous. Now there’s a daily risk of acid rain, or the seasonal temperature variations double, making the world fundamentally more inhospitable, or a new faction of enemies appears in the overworld that previously were only ever found in a special dungeon, or most of the previously ‘natural’ animals start developing into far more dangerous mutated varieties.
This sort of design allows you to make major shifts in difficulty and a general change of tone in an open procedural world that takes individual player pace and strategy into account - rather than using time to evolve the world, which tends to punish cautious strategies by ‘outrunning’ them.
In CDDA story terms, the easiest examples of these would be for the player to be completing research experiments from the labs, or implementing unfinished last-ditch plans/super weapons that the military was working on, or cooperating (or undermining) some major plan from a surviving NPC faction, or committing some crazy interaction with a set of portals and artifacts, again marginally guided by lost, last minute notes from some dead scientist or survivor - each of these could readily have major impacts on the world, and represent another unfolding ‘phase’ of the cataclysm.
It’s also fairly easy to seal some of the more interesting later game development behind these things. If I need to explore an Alpha-security lab with its lower level biology and tech books in order to hack the codes that I need to get into a Gamma-security lab with its higher level books or a Military Lab with its specialized CBM removal/installation tools, then I may not be able to move past the earliest steps of the Mutation development chain or the CBM development chain until I make it past some of these major game events.
