An ancient civilization known as the D'ni live in a parallel universe (realm) to Earth. The ancient D'ni can travel from realm to realm by writing books that describe another world and magically teleport the reader there. The authors of these magical texts do not actually create the worlds they describe but instead provide a magical passageway to those realms. Unfortunately, not all the D'ni are wise enough to make this distinction. One misguided novelist, Gehn, christens himself a creator, and subsequently lords over the realms he depicts like a god.

Myst's central character, Atrus, is not yet born when his earthling grandmother stumbles upon an ancient D'ni book that she uses to travel to a D'ni world and marry. Later, she returns to Earth to raise Atrus and tells him mythical tales about the D'ni people and the many realms. As Atrus gets older, he becomes increasingly skeptical about the D'ni civilization, suspecting it is simply the product of his grandmother's lively imagination.

These doubts are erased forever, though, when Atrus's father, Gehn, reenters his life and takes Atrus to the D'ni homeland. Soon Atrus realizes that his deranged and dangerous father is a complete megalomaniac, wreaking havoc on various parallel worlds, and he and his wife, Catherine, link to the safe haven of Myst island to raise two children. Unfortunately, their two children meet the same fate as Atrus's father. Corrupted by the power of the books, they too become seriously disturbed and troubled individuals.

At the end of Myst, you are met and recruited by Atrus. This is where Riven picks up. Atrus tells you of a land called Riven where his father, Gehn, has been left without means of escape for the past 33 years. Atrus also suspects that his wife, Catherine, is trapped somewhere on Riven, and he asks you to locate and rescue her. Atrus promises to join you and his wife once you locate her, and he gives you a route off Riven. He also warns you that Gehn is not to be trusted and hands you a mysterious device, commenting that the object will prove useful if you encounter Gehn. Next, you're put on Riven, left to explore and learn about it and its inhabitants, forming your own opinions as you progress.