There's something to do with the deep that everything shares, that much is obviously the entire point of the game. But I feel like there's something more. What are the hooded figures waiting for? If I remember right, they're waiting for something to arise.

What is the scientist a vessel for? The deep form says that each host has "no chance of surviving the deep". And whatever it is, it's trying to come up. Why? I doubt it's related to the leviathan, as it's shown it can surface whenever it would like.

So what is it? And its pretty clear that the "infection" that fish can have when you atrophy them is likely related to the ooze, as the ooze infects your fish.

Any chance that every single abberated fish is a result of this infection?

My theory is that the infection is a personification of something, or it has some sort of soul or spirit. It's trying to be free and reach the sky, but everything it infects falls to the deep. The starfish / fallen star pair from the pale reach gives that vibe to me. An ancient, ruthless deity is trying to climb up any way it can.