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The main storyline of No Man's Sky, also known as the Artemis Path, involves the player character uncovering the mysteries of Artemis and the Fourth Race, as well as the true nature of the Atlas, the Portals, and the universe of the game as a whole.
The other storyline is the Atlas Path, in which the player visits Atlas Interfaces and crafts Atlas Seeds to progress.
The game will switch between the three primary missions at the relevant times; to merge the three together into one cohesive story & allow you to gain quicksilver at certain parts of the story & new Atlas Seeds after each five milestones the player attains.