Protomatter is a highly-unstable and equally dangerous form of matter. While it can be used for other purposes, such as stellar re-ignition projects, Protomatter's unstable nature has seen to its more frequent use in destruction.
Perhaps the most famous - or infamous - use of protomatter was in the Genesis Project, in which the instability of protomatter caused the Genesis Matrix to fail and resulted in the accelerated life and death of the Genesis Planet in the Mutara Nebula in 2285. Protomatter was later used by Professor Gideon Seyetik in the reignition of star Epsilon 119 in 2370. On multiple occasions in the 2370's, protomatter was used in explosive devices, including an attempt by the Dominion to destroy the Bajoran sun using a Trilithium device combined with protomatter and tekasite.
In 2409, agents of Starfleet and the Romulan Republic discovered that the Hobus Supernova of 2387, instead of being a natural disaster, had actually been the result of a device - similar to that which the Dominion had attempted to use in 2373 - using protomatter, tekasite and decalithium having been fired into the Hobus sun by an agent of the Iconians.
- “Taris”: Investigating the Hobus System, a Starfleet Officer finds traces of protomatter, decalithium and tekasite used in the device that caused the supernova. Following forces loyal to Taris back to their base in the Iconia system, more of the three elements is discovered in a base where Taris is attempting to re-activate an Iconian gateway.
- “Coliseum”: Delta Recruits discover a piece of Iconian technology using protomatter and decalithium in Slamek's crashed ship.
- “Echoes of Light”: The player, along with Lukari Captain Kuumaarke discover that Draconis III in the 20 Draconis System has been devastated by a Tzenkethi protomatter bomb.
- “Of Signs and Portents”: The player, Kuumaarke and Rodek follow the trail of the weaponized protomatter.
- “Mirrors and Smoke”: Protomatter is used to scour, then revitalse, a Kentar moon.
- “Melting Pot”: The Tzenkethi attempt to use a protomatter device in the Dranuur System.
- “Scylla and Charybdis”: The player counters attempted protomatter attacks, including one on Bajor.
- “Turn the Tide”: The player disarms a number of protomatter warheads.
- “The Renegade's Regret”: Neth Parr recalls the earlier protomatter attacks throughout the Alpha Quadrant.
- “Gravity Kills”: The system is a protomatter farming site.
- “Tzenkethi Front”: The TFO centres around the capture of protomatter bombs.
- “Red Alert: Tzenkethi”
- Protomatter being used for beneficial purposes such as Project Genesis or Professor Seyetik's stellar re-ignition project, but also being capable of being used to destroy stars and planets makes it similar to Kal Dano's Quantum Phase Inhibitor, though any similarities seem to end there.
- System descriptions for the Xarantine System and the Oradhe System mention protomatter being found in micronebulas in the systems.