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.

The documentary chronicles the fall of the Atari Corporation through the lens of one of the biggest mysteries of all time, dubbed 'The Great Video Game Burial of 1983'. As the story goes, the Atari Corporation, faced with an overwhelmingly negative response to 'E.T.', the video game for the Atari 2600, disposed of hundreds of thousands of unsold game cartridges by burying them in the small town of Alamogordo, New Mexico.

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).

Evolution tells us that all life exists for only one purpose: to reproduce. But is that all there is? How could such a simple imperative lead us to create great art and civilizations? A new theory suggests that instead of passing on genes, our ultimate purpose is to process and pass on information. We are the universe figuring itself out. Scientists dig deep into DNA, chemistry, technology and engineering to find the meaning of life. One thing is certain: living is easier if you find a reason for living.

Beneath Jupiter's swirling clouds lie our solar system's deepest secrets: from its violent youth, through the birth of life to the death of the sun. Now, scientists are unlocking these secrets and discovering that every living thing exists thanks to Jupiter.

The theory of Némesis, a star that orbits the Sun and causes catastrophic events is explored. Nemesis is a hypothetical red dwarf or brown dwarf, originally postulated in 1984 to be orbiting the Sun at a distance of about 95,000 AU (1.5 light-years) somewhat beyond the Oort cloud, to explain a perceived cycle of mass extinctions in the geological record, which seem to occur more often at intervals of 26 million years.