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.

Beginning with the separation of the fuzzy thinking and pious fraud of astrology from the careful observations of astronomy, Sagan follows the development of astronomical observation. Beginning with constellations and ceremonial calendars (such as those of the Anasazi), the story moves to the debate between Earth and Sun-centered models: Ptolemy and the geocentric worldview, Copernicus' theory, the data-gathering of Tycho Brahe, and the achievements of Johannes Kepler (Kepler's laws of planetary motion and the first science-fiction novel).

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.

Following the wildly successful 'Cosmos: A Spacetime Odyssey,' Neil deGrasse Tyson returns as host to translate more revelations of science into a lavish transporting experience, taking audiences on a series of spiritual voyages of exploration. The show reveals previously uncharted realms, including lost worlds, worlds yet to come, and the worlds that humans may one day inhabit. Ann Druyan, original creative collaborator to Carl Sagan, whose iconic docuseries 'Cosmos' provided inspiration for this series, serves as executive producer alongside Seth MacFarlane.
Episode 1 takes viewers on a wild ride with the Ship of Imagination in an adventure spanning billions of years into the evolution of life.

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).