Maybe Subnautica ? It all takes place in an alien ocean, starting with you having to hold your breath to swim down to coral reefs for resources and at the end you are piloting a submarine to the deepest, darkest depths of the ocean. It has some base building to it as well, is this the kind of game you are looking for?

I've played Minecraft, but all the mod packs I've played have been like assorted bundles. Big mix of automation, magic, quality of life, and other stuff. I've never tried one like what you described, and I also haven't played Hytale or Vintage Story so I can't really help you out there