The directive also authorized the use of any and all means to destroy an Omega molecule. This made the Omega Directive the only known order to supersede the Prime Directive. The Omega Directive was deemed necessary because of the extreme power and the threat to interstellar civilization posed by even a single molecule. Knowledge of the Omega molecule and the Omega Directive was restricted to Starfleet officers ranking captain or higher.
In 2269, a team of 127 Federation scientists, led by Professor Ketteract, were working on a top secret experiment entitled "Project Omega" at a classified research center in the Lantaru sector. The project's goal was to create an inexhaustible energy source which would end all needs for all other sources of energy, hence the name Omega. The research showed a single molecule of Omega contained the same power as a warp core, which led Ketteract to believe a small chain of Omega molecules could sustain a civilization indefinitely. Ketteract, along with various cosmologists, theorized that the Omega molecule once existed in nature for an infinitesimal period of time at the exact moment of the big bang. Ketteract even postulated that Omega was the primal source of energy for the explosion that began our universe.
The scientists were able to synthesize a single Omega molecule, but only for a fraction of a second before it destabilized, destroying the research center and killing all 127 scientists. An unexpected secondary effect was the rupture of subspace within several light years, causing warp travel to become an impossibility within this area. Starfleet Command realized the terrible implications: a chain reaction involving a handful of Omega molecules could devastate and/or destroy subspace throughout an entire quadrant. This would effectively end interstellar travel for spacefaring civilizations in the quadrant. If such an event happened within Federation space, all speedy communication, transport and trade between Federation worlds would be rendered impossible; thus the Federation's basic ability to function as a working entity would be severely curtailed.
Therefore Starfleet Command suppressed all knowledge of the experiment and fabricated the story of a natural phenomenon occurring in the Lantaru sector which made warp travel impossible within the seven-light year radius of subspace devastated by the Omega explosion.
Starfleet then enacted the Omega Directive, naming it after the last letter in the Greek alphabet, chosen to signify the molecule as the ultimate threat not only to the Federation but to every spacefaring civilization in the entire galaxy. If a starship were to detect an Omega molecule, the following procedure would occur: the ship's computer would disengage the engines immediately and lock out all computer access, displaying the Greek letter "omega" on every bridge console. Only the captain would be able to disable the lockout. In the privacy of his or her ready room or other secured area, with the doors locked, he or she would give the computer the proper high-level security authorization code to access the sensor data. The computer would brief the captain regarding the detection of Omega molecules, and then give instructions to implement the Omega Directive immediately – disregarding all other priorities, including the Prime Directive. The captain, absolutely forbidden from discussing anything about what was happening with any member of his/her crew, would contact Starfleet Command and inform them of the situation. Starfleet Command would then dispatch in a specialized team authorized to use whatever means necessary to destroy the molecules. (VOY: "The Omega Directive")
The only known execution of the Omega Directive occurred in the Delta Quadrant on stardate 51781.2 in 2374 by Captain Kathryn Janeway, commanding officer of the USS Voyager. On that stardate, Voyager's sensors encountered the shock wave from a nearby Omega explosion, revealing the presence of one or more Omega molecules in the vicinity. However, Voyager was completely out of contact with Starfleet when the detection occurred, with no contact possible in the foreseeable future. Complicating the matter was the fact that Seven of Nine was aware of the molecule's existence (due to the Borg's own Omega experiments, and because the Borg had assimilated Starfleet captains and therefore have all of their knowledge). Unable to call for an Omega team to deal with the problem, Janeway therefore adapted the directive to the situation. Janeway briefed her senior staff on the directive and worked with them to destroy the molecules. The Voyager crew successfully destroyed the Omega molecules. (VOY: "The Omega Directive")
The Omega Directive is mentioned by Captain James T. Kirk in the 2006 video game Star Trek: Legacy after a devastating attack spreads thousands of Omega particles into a star system. Kirk asked Starfleet to develop the directive.
The game Star Trek: Armada depicts events of an Omega molecule. It was found by the Ferengi, who were preparing to sell it to the Cardassians, as they did not realize its power. The Romulans led by Sela captured it and hid it at a Romulan starbase where the Borg assimilated it. It was moved to Unimatrix 01 where an invasion force led by the Federation-Klingon-Romulan alliance destroyed it and the surrounding Borg sectors.