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I had the exact same problem. I saw that lava castle and two big baddies swimming around it. No sign of aliens.
I'd never imagine the alien base was there. Instead i went exploring further and found the containment facility.<…
How was i supposed to find the alien thermal plant? Only clues i had were: volcanic area, 1200m deep. Did i miss any other clue?
I did find an alien structure but it was unrelated. Frustrated as hell i had to google the location.
Well, i think i'm in the same point in the story.
I have a data bank entry about alien bases. It gives a rough description about where it could be. The one i probably need to visit to progress the story. That's what i'm exploring now.