Inside the world-renowned physics laboratory Fermilab, a team of scientists are constructing an audacious experiment to hunt for a mysterious new ‘ghost’ neutrino. If they find it, this could transform our understanding of the nature and fabric of our universe. The problem is, these tiny particles are almost impossible to detect.
Elsewhere, physicists conduct experiments in some of the most extreme environments on the planet: from deep mine shafts in South Dakota to vast ice fields at the South Pole. In these unlikely places supersized neutrino detectors hope to unlock the universe’s deepest secrets. Could neutrinos overturn the most precise theory of particle physics that humans have ever written down? Could they even be a link to a hidden realm of new particles that permeate the cosmos – so called dark matter? Scientists at Fermilab are edging towards the truth.

Our world, our solar system, our universe, none of it would exist without a ghostly particle called the neutrino. They are our early warning system whenever there's trouble in the universe. Neutrinos trigger star-killing explosions, supernovas. Neutrinos can answer so many questions, from why do we exist to how was the universe created. Neutrinos can be the very reason that we exist at all. The more we understand these elusive particles, the more we can gain insight into how the universe works.

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.

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.