Related to my previous post, some people seemed to think I was mistaken on my capital being my capital or if the event actually happened, so I went back and recorded the event to hopefully clear up confusion.
Basically just had to complain as I just downloaded the machine age dlc finally and forced cetana to spawn as the end game to try it out.
I was majorly enjoying the new content and preparing myself for a very early game 2x crisis, never even saw it.
Without warning, my homeworld, home system, my main shipyard and half my fleets just disappear. No fight, no event, just deleted. Reloaded to try and save it and see if it was a random event but it is garunteed lost to a currently uninteractable nanite swarm, as nanite ascended robots which makes sense. I thn proceed to loose 2 more core very important systems with no event to try and stop or even explain it, and lost over half my economy. NPCs instantly start war with me, and I just completely lost interest in the game within 30 minutes of play time.
Quick google told me it was cetana and apparently she can just wipeout fallen empires by spawning in, I just got really unlucky. Any end game mechanic that can just delete a massive portion of player power with no way to fight back or avoid it tho is really bad mechanics imo. I didnt even see the actual end game, just got deleted into subserviance of my neighbor through game code, now they are fighting. Good times.
Quick edit since Ive read some comments: can definitely say the only FE had all its systems on the other side of the small galaxy I was on. Sounds like it may have just been a glitch which means I can try again without fear of this happening, but yah super weird.
Second Edit: I had the Origin that gave me a relic world for start, could that have been the cause?