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).

Professor Jim Al-Khalili continues his investigation of the atom by looking at radioactivity, the Atom Bomb and the Big Bang, and even why we are here and how we were made. He shows that, in the quest to understand the atom, the mystery of how the entire universe was created became revealed

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 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.

Could we be unique in the universe or is there another planet similar to earth somewhere in the cosmos? Is it possible that Alpha Centauri, our nearest star, is home to another earth-like planet? Earth sized planets have been hard to find, but indirect methods are coming on line to give scientists a good survey of how many such bodies may be in the universe. How rare would it be to find life on another earth-like planet?

In episode two, Professor Brian Cox is off to India, where he assesses arguably the first evidence of rational thought in literature, the poetry of the Vedic monks. They pondered mankind's origins, realising there must have been a day with no yesterday - a day of creation - prompting the age-old question of where did the universe come from? Brian marvels that the universe seems to follow a set of rules, the laws of physics, allowing space to be considered on the grandest scale, travelling to the most distant, farthest reaches of the cosmos just by using our minds. Brian also visits Japan, and offers viewers the idea that man lives in just one of an infinite number of universes that are being made all the time.