Carl Sagan opens the program with a description of the cosmos and the Spaceship of the Imagination. The ship journeys through the universe's hundred billion galaxies, the Local Group, the Andromeda Galaxy, the Milky Way, the Orion Nebula, our Solar System, and finally the planet Earth. Eratosthenes' successful calculation of the circumference of Earth leads to a description of the ancient Library of Alexandria. Finally, the Ages of Science are described, before pulling back to the full span of the Cosmic Calendar.

Famed astrophysicist Neil deGrasse Tyson takes a tour of the Solar System and the known universe establishing the components of Earth's "address" within the Virgo Supercluster. He then shares the story of the person who championed an expansive understanding of Earth's place in the universe by presenting Renaissance Italian Giordano Bruno's vision of the universe as a limitless expanse of space and time. He then makes an exploration into the Cosmic Calendar, which dates back to the dawn of the Big Bang (similar to the presentation from episode 1 of the original series). The episode ends with deGrasse Tyson narrating how he met his mentor Carl Sagan, who hosted the first Cosmos series.

Ideas about time and space are explored in the changes that constellations undergo over time, the redshift and blue shift measured in interstellar objects, time dilation in Albert Einstein's theory of relativity, the designs of both Leonardo da Vinci and spacecraft that could travel near light speed, time travel and its hypothetical effects on human history, the origins of the Solar System, the history of life, and the immensity of space. In Cosmos Update, the idea of faster-than-light travel by wormholes (researched by Kip Thorne and shown in Sagan’s novel Contact) is discussed.

Sagan discusses the story of the Heike crab and artificial selection of crabs resembling samurai warriors, as an opening into a larger discussion of evolution through natural selection (and the pitfalls of intelligent design). Among the topics are the development of life on the Cosmic Calendar and the Cambrian explosion; the function of DNA in growth; genetic replication, repairs, and mutation; the common biochemistry of terrestrial organisms; the creation of the molecules of life in the Miller-Urey experiment; and speculation on alien life (such as life in Jupiter's clouds). In the Cosmos Update ten years later, Sagan remarks on RNA also controlling chemical reactions and reproducing itself and the different roles of comets (potentially carrying organic molecules or causing the Cretaceous–Paleogene extinction event).

Sagan reflects on the future of humanity and the question of 'who speaks for Earth?' when meeting extraterrestrials. He discusses the very different meetings of the Tlingit people and explorer Jean-François de La Perouse with the destruction of the Aztecs by Spanish conquistadors, the looming threat of nuclear warfare, and the threats shown by destruction of the Library of Alexandria and the murder of Hypatia. The episode ends with an overview of the beginning of the universe, the evolution of life, and the accomplishments of humanity and makes a plea to mankind to cherish life and continue its journey in the cosmos. The Cosmos Update notes the preliminary reconnaissance of planets with spacecraft, the fall of the Berlin Wall and the end of apartheid in South Africa, and measures towards the reduction of nuclear weapons.

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