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.

Beginning with the origins of the universe in the Big Bang, Sagan describes the formation of different types of galaxies and anomalies such as galactic collisions and quasars. The episodes moves further into ideas about the structure of the Universe, such as different dimensions (in the imaginary Flatland and four-dimensional hypercubes), an infinite vs. a finite universe, and the idea of an oscillating Universe (similar to that in Hindu cosmology). The search into other ideas such as dark matter and the multiverse is shown, using tools such as the Very Large Array in New Mexico. Cosmos Update shows new information about the odd, irregular surfaces of galaxies and the Milky Way perhaps being a barred spiral galaxy

Questions are raised about the search for intelligent life beyond the Earth, with UFOs and other close encounters refuted in favor of communications through SETI and radio telescope such as the Arecibo Observatory. The probability of technically advanced civilizations existing elsewhere in the Milky Way is interpreted using the Drake equation and a future hypothetical Encyclopedia Galactica is discussed as a repository of information about other worlds in the galaxy. The Cosmos Update notes that there have been fewer sightings of UFOs and more stories of abductions, while mentioning the META scanning the skies for signals.

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 Land of the Cave Bear, Alice ventures to the parts of the northern hemisphere, hit hardest by the cold - Europe and Siberia. High in the mountains of Transylvania, a cave sealed for thousands of years reveals grisly evidence for a fight to the death between two staving giants, a cave bear and a cave lion. Yet Alice discovers that for woolly rhinos and woolly mammoths, the Ice Age created a bounty. The Mammoth Steppe, a vast tract of land which went half way round the world, provided food all year round, for those that liked the cold. It was these mammoths that Europe's most dangerous predators hunted for their survival.

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.