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Protomatter was an unstable substance that could be used for a variety of purposes. Due to its volatile nature, however, it was considered highly controversial. (Star Trek III: The Search for Spock; DS9: "Second Sight"; VOY: "Mortal Coil")
During the 23rd century, protomatter was a highly-controlled substance in the Federation. In the 2380s, Dr. David Marcus secretly used protomatter in the construction of the Genesis device, which resulted in an unstable matrix and the ultimate failure of Project Genesis. Dr. Marcus had acquired the protomatter from rogue Starfleet Admiral Androvar Drake, who gave it to him in hopes of developing Genesis into a weapon. (Star Trek III: The Search for Spock, TOS novel: The Ashes of Eden)
Professor Gideon Seyetik successfully used protomatter to reignite the dead star Epsilon 119 near the Bajoran sector. Dr. William Hoesch would study Seyetik's work as part of the development of his own Genesis device. (DS9: "Second Sight", Star Trek: Pendragon: "Diluvium")
Protomatter could also be a deadly weapon. It was used as an explosive, or part of various explosive devices, by many different terrorist groups. The Maquis used a protomatter-based explosive to destroy the Cardassian freighter Bok'nor in 2370. As part of the prelude to the Dominion War, a Founder disguised as Dr. Julian Bashir nearly destroyed the Bajoran system with a protomatter-trilithium device in 2373. (DS9: "The Maquis, Part I", "By Inferno's Light")
Naturally-occurring protomatter was discovered in a nebula in the Delta Quadrant by the USS Voyager. The Voyager crew attempted to use it as a power source, but these efforts resulted in the (temporary) death of Neelix. (VOY: "Mortal Coil")
The Romulans had experience with protomatter going back at least as far as the 22nd century, and by the 2380s, the Tal Shiar was developing a stockpile of protomatter-based weaponry. (Star Trek: Pendragon: "A Quiet Darkness")