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|There is more information available on this subject at Deuterium on the English Wikipedia.|
Deuterium is an isotope of the chemical element Hydrogen (chemical symbol H). Hydrogen contains only one proton in its nucleus. Protium contains only the proton, deuterium's nucleus contains one neutron in addition to the proton, and tritium contains two neutrons. Deuterium nuclei produce a great deal of energy when fused together into helium nuclei. This is the fusion reaction that occurs in the sun and all other stars. So, deuterium is a primary fuel source for Covenant starship reactors.
Deuterium has a natural abundance on planet surfaces, such as on Earth and Pegasi Delta. The Covenant build refineries to refine this material for use in their ships. It is also used in UNSC stations, most likely to power the onboard reactors and, should the need arise, facilitate self-destruction by flooding the reserve tanks into the reaction chamber.