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.

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

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.

This episode explores the wave theory of light as studied by mankind, noting that light has played an important role in scientific progress, with such early experiments from over 2000 years ago involving the camera obscura by the Chinese philosopher Mozi. Tyson describes the work of the 11th century Arabic scientist Ibn al-Haytham, considered to be one of the first to postulate on the nature of light and optics leading to the concept of the telescope, as well as one of the first researchers to use the scientific method. Tyson proceeds to discuss the nature of light as discovered by mankind. Work by Isaac Newton using diffraction through prisms demonstrated that light was composed of the visible spectrum, while findings of William Herschel in the 19th century showed that light also consisted of infrared rays. Joseph von Fraunhofer would later come to discover that by magnifying the spectrum of visible light, gaps in the spectrum would be observed. These Fraunhofer lines would later be determined to be caused by the absorption of light by electrons in moving between atomic orbitals when it passed through atoms, with each atom having a characteristic signature due to the quantum nature of these orbitals. This since has led to the core of astronomical spectroscopy, allowing astronomers to make observations about the composition of stars, planets, and other stellar features through the spectral lines, as well as observing the motion and expansion of the universe, and the existence of dark matter.

This episodes the nature of the cosmos on the micro and atomic scales, using the Ship of the Imagination to explore these realms. Tyson describes some of the micro-organism that live within a dew drop, demonstrating parameciums and tardigrades. He proceeds to discuss how plants use photosynthesis via their chloroplasts to convert sunlight into chemical reactions that convert carbon dioxide and water into oxygen and energy-rich sugars. Tyson then discusses the nature of molecules and atoms and how they relate to the evolution of species. He uses the example set forth by Charles Darwin postulating the existence of the long-tongued Morgan's sphinx moth based on the nature of the comet orchid with pollen far within the flower. He further demonstrates that scents from flowers are used to trigger olfactory centers in the brain, stimulating the mind to threats as to aid in the survival of the species. Tyson narrates how Greek philosophers Thales and Democritus postulated that all matter was made up of combinations of atoms in a large number of configurations, and describes how carbon forms the basic building block for life on earth due to its unique chemical nature. Tyson explains on the basic atomic structure of protons, neutrons, and electrons, and the nature of nuclear fusion that occurs in most stars. He then discusses the existence of neutrinos that are created by these nuclear processes in stars, and that detecting such sub-atomic particles which normally pass through matter require subterranean facilities like the Super-Kamiokande that were used to detect neutrinos from the supernova SN 1987A in the Large Magellanic Cloud before light from the explosion were observed due to their ability to pass through matter of the dying sun. Tyson compares how neutrinos were postulated by Wolfgang Pauli to account for the conservation of energy from nuclear reactions in the same manner as Darwin's postulate on the long-tongued moth. Tyson concludes by noting that there are neutrinos from the Big Bang still existing in the universe but due to the nature of light, there is a "wall of infinity" that cannot be observed beyond.

This episode is centered around how science, in particular the work of Clair Patterson (voiced in animated sequences by Richard Gere[33]) in the middle of the 20th century, has been able to determine the age of the Earth. Tyson first describes how the Earth was formed from the coalescence of matter some millions of years after the formation of the Sun, and while scientists can examine the formations in rock stratum to date some geological events, these can only trace back millions of years. Instead, scientists have used the debris from meteor impacts, such as the Meteor Crater in Arizona, knowing that the material from such meteors coming from the asteroid belt would have been made at the same time as the Earth. Patterson also examined the levels of lead in the common environment and in deeper parts of the oceans and Antarctic ice, showing that lead had only been brought to the surface in recent times. He would discover that the higher levels of lead were from the use of tetraethyllead in leaded gasoline resulting in government-mandated restrictions on the use of lead.