This post spoils the core gameplay and player progression in Subnautica, but not the specific story nor scripted plot events.
Subnautica is a long open world survival game set in a vast deep ocean. In it, you have to forage for food, manage your oxygen when diving into caves and deep sea trenches, and collect resources to build your own underwater base(s) and submarine(s) to find out What Really Happened Here.
Much like the other first person indie survival game The Long Dark, Subnautica features no combat, no world map, and essentially no NPCs or quests to complete for anyone. The few lethal weapons are either cumbersome and annoying to maintain (poison gas torpedoes must be crafted and loaded) or practical but anti-juicy (your knife)... but most importantly, unlike The Long Dark's focus on hunting, killing creatures in Subnautica *never* yields any reward or drops -- even when the game confusingly asks you to collect shark teeth but killing sharks never yields any shark teeth.
(Why? Well, there's a few story threads about how use of force cannot get you what you want, as well as a faint anti-capitalist / anti-colonialist message. But the smoking gun of authorial intent is in the credits: a dedication to the families of
Newtown, Connecticut. The design lead has also
talked about their no-gun philosophy.)
PC Gamer already did a nice roundtable about Subnautica's early climactic story moment, so instead I want to focus on Subnautica's most interesting systemic feature: its depth-based 3D level design, and implications on the rest of the game.