Beginning with the origins of the universe in the Big Bang, Sagan describes the formation of different types of galaxies and anomalies such as galactic collisions and quasars. The episodes moves further into ideas about the structure of the Universe, such as different dimensions (in the imaginary Flatland and four-dimensional hypercubes), an infinite vs. a finite universe, and the idea of an oscillating Universe (similar to that in Hindu cosmology). The search into other ideas such as dark matter and the multiverse is shown, using tools such as the Very Large Array in New Mexico. Cosmos Update shows new information about the odd, irregular surfaces of galaxies and the Milky Way perhaps being a barred spiral galaxy

The film intends to illustrate the birth and death of an undiscovered universe, with powerful images, from the Big Bang to the Mesozoic era and through the present and beyond. Based on a project conceived decades ago, the documentary is highly experimental and perhaps Terrence Malick's most ambitious film, described by the director himself as 'one of my greatest dreams.'