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They have that handled by end game disasters... each choice you make, be it research or decisions in planets you discover, has a risk of triggering the disaster... it has been teased that it could be robotic uprising, opening a hole to another dimension, waking up an ancient insectoid master race...
it does, however they did tease about large ancient and advanced empire that lie dormant since they evolved passed meddling into inferior races, they hold special tech that you will have trouble defeating and will be a fearsome for if triggered, but if you reverse engineer they tech, you get some special boons :)

About ancient empires, there was a line on the wiki that current expanding space faring empires can also become fallen empires. Not sure how that mechanic would work vis a vis universe generation.
 
About ancient empires, there was a line on the wiki that current expanding space faring empires can also become fallen empires. Not sure how that mechanic would work vis a vis universe generation.
Haven´t seen that one, but could figure it´s something to do with AI coding... Wiz seems to have made some new programming and AI coding for Stellaris as far as I recall, which is also used in HOI and the reason he is helping out there in these days... But figure it´s a matter of chance whenever a race gets too much ahead or reaches a certain point... They did announce that some techs have the chance of spawning disasters, like robotic AI gone rogue, so would go along that line to have it spawn a dormant, fallen empire :)
 
It may have something to do with internal rebellions and factions. Perhaps if the local pops become too withdrawn from the galaxy they can force the empire to adopt a stasis of X years, which if not resolved via civil war, will turn permanent. Sort of like CK2's factions demanding that you step down for your heir.

Since I seem to remember that they also referred to the "player's empire" as becoming a Fallen empire potentially too.