S. Darko follows Samantha Darko, the younger sister of Donnie, the protagonist of Donnie Darko, and her friend Corey. On their way to California, their car breaks down, forcing them to wait in a small town until it is fixed. While there, Samantha begins to have dreams that warn her of the end of the universe.
Donnie Darko's little sister Samantha and her best friend Corey are on a cross-country road trip, but soon find themselves entangled in a dangerous glitch in the time-space continuum.