So have they ALWAYS been in this system and probably always will be does anyone know?
No, they have not. When I started the game, there were no Thargoids at all, anywhere. A couple years later, the first crashed Thargoid ship was discovered, and there was a big hoo-ha about it. It was in several pieces strewn about, and no one knew how they fit together.
This was my favorite reconstruction attempt. Not terrible, really, but pretty funny to see now
After more time passed, the very first Thargoid hyperdiction happened, and that was in the Pleiades. That made big news!
We all went rushing out there to jump back and forth for hours until we got hyperdicted, too (it was a random event, and not very common). At the time each hyperdiction was exactly the same, like an in-game cut scene. The Thargoids were not aggressive, and they just looked us over while we looked them over.
After that, there was a very long period (years) during which the story slowly unfolded, the Non-Human USS's were introduced, and Scouts could be found, and eventually larger Thargoids as well. All of those are still there, following the old rules of Thargoid combat.
And now we have the arrival of the Maelstroms and the increase in Thargoid aggressiveness, as the war unfolds.
It's been a pretty interesting story, although it happens very slowly
