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Deuterium, along with its antimatter opposite, antideuterium, is the primary fuel used in matter-antimatter reactions, such as those generated in warp cores, and was stored in large tanks aboard starships for this purpose. (TNG: "Heart of Glory", "Captain's Holiday", "Final Mission", "Night Terrors", "Unification I", and more, et al.)
The Bussard collectors on some starships were used to collect hydrogen and interstellar gasses, including deuterusium. (TNG: "Samaritan Snare"; VOY: "Unforgettable", "The Haunting of Deck Twelve") However, the USS Voyager occasionally needed to find deuterium from other sources. (VOY: "The Cloud", "Demon", "Bliss")
In 2369, Chief O'Brien ordered that the deuterium flow to carbon reaction chamber two should be increased by five percent; however, the station's computer refused to do this and told O'Brien to read the Cardassian operational guidelines. (DS9: "The Forsaken")
In 2371, Miles O'Brien and Jake Sisko investigated the possibility of turning the ore processing section of Deep Space 9, formerly used for processing uridium using Bajoran slave labor, into a deuterium refinery. They accidentally triggered Dukat's counter-insurgency program while doing so, however. (DS9: "Civil Defense")
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