Ocean by Steven Utley

Ocean by Steven Utley (Fantastic, August 1976) opens with the female narrator, who has “flippers and gills now”, poisoned by the spines of a sea urchin—but she escapes its effects by surfacing and becoming a flying creature.
The next section describes an ongoing struggle she is having with a man who is either (a) interfering with her (possibly prosthetic) body, or (b) operating her controls (she may be a spaceship), or (c) she is a personality living in a ship’s computer. Later we learn (spoiler) that it is the latter, and that she is on a generation ship where everyone died apart from her. When she got old she uploaded into the ship’s circuits/memory, and at that point sensed a malevolent entity.
The story ends with some sort of reckoning.
Trying to work out what was going on while reading this story was like wading through mud.
– (Awful). 2,700 words. Story link.