The scariest thing to me was to discover that all is gone. Humanity is perished only to download their brains on some PC that orbits in the sky waiting for sentient aliens to find it before they go mad, and somehow restores them or people by some coded DNA, that the only thing left - is just one single dying woman, insane AI that tries to save what once was humane but now are robots, or agonizing living corpses that are dopamine addicts on top of that and finally that I am a robot, and i will stay here will all this mess forever until the batteries will die, and i have no technical proficiency to restore my only friend, that I non-intentionally killed. And I can do NOTHING about all of that.
Despair. Loneliness. Existential fear. THAT was the scariest part for me

first construct encounter personally. Akers are probably 2nd scariest, and everything else were forgettable bland encounter that could be removed without any loss.
I generally felt that while as a philosophical fiction and think-piece, SOMA is phenomenal work of art.
but, as a horror game it was not a good. kinda bad tbh.

The ending prior to the Ark section.

The underwater part with the big fish if I remember right was really scary,but the ending,the blackness of it,wow.

The proxies of Akers are much more disturbing, those choking sounds and that screech...