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.

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).

At 11 o'clock on New Year's Eve of the Cosmic Calendar, Homo erectus stood up for the first time, freeing its hands and earning the species its name. They began to move around, to explore, daring to risk everything to get to unknown places. Our Neanderthal relatives lived much as we did and did many of the things we consider to be 'human.' More restless than their cousins the Neanderthals and Denisovans, our Homo sapiens ancestors crossed seas and unforgiving landscapes, changing the land, ocean and atmosphere, leading to mass extinction. The scientific community gave our age a new name, 'Anthropocene.'
Since the first civilizations we've wondered if there's something about human nature that contains the seeds of our destruction. Syukuro Manabe was born in rural Japan and took an intense interest in Earth's average global temperature. In the 1960's, he would assemble the evidence he needed to predict the increase of Earth's temperature due to greenhouse gases until it becomes an uninhabitable and toxic environment, leading to our extinction. 'This doesn't have to be,' says Neil deGrasse Tyson, 'it's not too late. There's another hallway, another future we can still have; we'll find a way.'