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An Omega molecule, also called the Omega particle and Particle 010, was a highly unstable and short lived molecule that was known to exist within the universe.
The sheer power of the particle meant that a single stable molecule was capable of generating the same power output as a warp core. Furthermore, it was believed that up to 200 million molecules were sufficient to devastate an entire quadrant within a galaxy.
It was believed that if it could be artificially recreated then it would be a powerful substance that was capable of powering an entire civilization.
It was theorized that it existed in nature at the instant of the Big Bang.
A single Omega molecule was synthesized in 2268 by Federation physicist Dr. Bendes Kettaract. It remained stable for a fraction of a second before exploding, killing 127, destroying the research station and rupturing subspace for several light years in the Lantaru sector, making warp travel and subspace communications impossible. (VOY episode: "The Omega Directive"; TOS - Section 31 novel: Cloak)
It was later determined this incident was orchestrated by an assimilated Vulcan named T'Uerell. She was able to stabilize an Omega molecule and used it to power a Borg sphere, which was destroyed by James T. Kirk. Kirk thereafter recommended the establishment of the Omega Directive, ordering the destruction of Omega molecules whenever discovered, and limiting knowledge of the molecule to starship captains and flag officers. The event was later known as the Kettaract Incident. (ST video game: Legacy)
The Borg learned of the Omega molecule (known to them as "Particle 010") through the assimilation of several species. They regarded Omega with near-reverence, believing it to be a perfect and flawless substance that if assimilated would grant them perfection as well. They were able to synthesize a single molecule, which destroyed 29 Borg vessels with 600,000 drones when it destabilized. All Borg were ordered to assimilate any Omega molecules found.
In 2374, the USS Voyager discovered a civilization in the Delta Quadrant which was successful in synthesizing some 200 million stable Omega molecules.Voyager managed to neutralize the molecules before they could do any further damage to subspace.The remaining Omega molecules were destroyed by a modified gravimetric torpedo. (VOY episode: "The Omega Directive")
Species 8472 were noted as using omega molecules as powerful weapons of mass destruction in alternate timelines during their war against the Borg Collective. In one timeline, this resulted in the large scale destruction of Borg space with the remaining vessels restricted to sublight. (VOY novel: Places of Exile)
In 2376, the Borg, led by a clone of Locutus, attacked the Federation, Klingon Empire, and Romulan Star Empire in an attempt to obtain an Omega particle. They were eventually stopped and destroyed by the USS Enterprise-E. (ST video game: Armada)
The Caeliar used an Omega Molecule Generator to power their city-ships. The power output of this device was capable of forming several subspace tunnels simultaneously, maintaining the city-ships quantum field and various other functions. During the Borg Invasion of 2381, Federation Captains Jean-Luc Picard, William Riker, Ezri Dax and Earth Starfleet Captain Erika Hernandez formulated a plan to use the Omega Molecule Generator of the Caeliar City-ship Axion to lure the entire Borg armada to the Azure Nebula where they were absorbed into the Caeliar Gestalt. (ST - Destiny novel: Gods of Night)
During their return to the Delta Quadrant, the Project Full Circle fleet learned that the Omega molecule did indeed trigger the Big Bang, and is increasingly building power and stability in a sub-dimension known as the Omega Continuum, essentially 'counting down' to the end of this universe. It was discovered that the Omega Continuum is made out of pure Omega molecules, and that the Omega particles sought by the Borg and used by the Caeliar are in fact synthetic, imperfect versions of Omega.
When a civilian scientist expedition encountered a rift into this dimension, they unintentionally accelerated the universe's decay as their matter provided Omega with additional energy, but the instability caused by this chain reaction also created the Q Continuum, the Q serving as a creative force to 'counter' the destructive potential of the Omega Continuum. Although Q believed that the only way to stop the decay would be to reverse the original incident and thus essentially erase the Q Continuum from existence, Voyager was able to repair the disruption while only shortening the universe's lifespan by a few million years as opposed to the trillions they would have lost previously, thus saving the Q, but this is only achieved through the sacrifice of Captain Afsarah Eden- a 'child' of the Omega Continuum created when the continuum manifested a new entity based on a scientist who discovered it- and Q's son, who possessed the potential to channel the power of Omega and contain it once again. (VOY novel: The Eternal Tide)