In the second stop in his exploration of the wonders of the universe, Professor Brian Cox goes in search of humanity's very essence to answer the biggest questions of all: what are we? And where do we come from? This film is the story of matter - the stuff of which we are all made. Brian reveals how our origins are entwined with the life cycle of the stars. But he begins his journey here on Earth. In Nepal, he observes a Hindu cremation. Hindu philosophy is based on an eternal cycle of creation and destruction, where the physical elements of the body are recycled on to the next stage. Brian draws a parallel with the life cycle of the stars that led to our own creation. Next, he explains how the Earth's resources have been recycled through the ages. How every atom that makes up everything we see, was at some time a part of something else. Our world is made up of just 92 elements, and these same 92 elements are found throughout the entire universe. We are part of the universe because we are made of the same stuff as the universe.

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

In the fifth episode of the series, Morgan Freeman sets to examine the nature of evil, visiting a serial killer in prison and witnessing an exorcism in India. He also explores ancient beliefs, including Zoroastrianism.