The simple act of making an apple pie is extrapolated into the atoms and subatomic particles (electrons, protons, and neutrons) necessary. Many of the ingredients necessary are formed of chemical elements formed in the life and deaths of stars (such as our own Sun), resulting in massive red giants and supernovae or collapsing into white dwarfs, neutron stars, pulsars, and even black holes. These produce all sorts of phenomena, such as radioactivity, cosmic rays, and even the curving of spacetime by gravity. Cosmos Update mentions the supernova SN 1987A and neutrino astronomy.

The idea of intelligence is explored in the concepts of computers (using bits as their basic units of information), whales (in their songs and their disruptions by human activities), DNA, the human brain (the evolution of the brain stem, frontal lobes, neurons, cerebral hemispheres, and corpus callosum under the Triune Brain Model), and man-made structures for collective intelligence (cities, libraries, books, computers, and satellites). The episode ends with speculation on alien intelligence and the information conveyed on the Voyager Golden Record.

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.

Richard Dawkins examines the growing suspicion the public has for science-based medicine, despite its track record of successes like the germ theory of disease, vaccines, antibiotics and increased lifespan. He notes a fifth of British children are currently not immunised against measles, mumps and rubella, attributing it to fears arising from a highly controversial report linking the vaccine with autism. Dawkins criticizes the growing field of alternative medicine which does not pass the same objective and statistical rigour as scientifically derived treatments using controlled double-blind studies. Without verifiable evidence, alternative therapies must rely on biased anecdotes and word of mouth to perpetuate. Dawkins observes these treatments have fanciful rationales and rituals behind them, with many alternative treatments employing pseudoscientific jargon such as "energy", "vibration" or "quantum theory" to give themselves greater credence to patients.

In the final part, Professor Al-Khalili uncovers tales of success and heartache in the story of chemists' battle to control and combine the elements, and build our modern world. He reveals the dramatic breakthroughs which harnessed their might to release almost unimaginable power, and he journeys to the centre of modern day alchemy, where scientists are attempting to command the extreme forces of nature and create brand new elements.

Long ago, two species of human beings coexisted on Earth until competition drove one of them to extinction. This program, set in the southwest of France 35,000 years ago, reconstructs the life in the Neanderthal world at the time Cro-Magnons first entered the scene. All aspects of Neanderthal clan life are examined, including tool- and weapon-making, hunting and gathering, health and healing, childbirth, rituals, and making fire. Footage of skeletal remains and the scholarly research of eminent paleontologist Chris Stringer and Oxford University's Paul Pettitt support the documentary.