The directive also authorized the use of any and all means to destroy an Omega molecule, superseding any and all other regulations, up to and including but not limited to the Prime Directive. The Omega Directive was deemed necessary because of the extreme power and consequently catastrophic threat to interstellar civilizations posed by even a single molecule. Knowledge of the Omega molecule and the Omega Directive was restricted to starship captains and flag officers. Captains received training on how to deal with the issue.
In the mid-23rd century, a team of 127 top-Federation scientists, led by the Starfleet physicist Ketteract, was working on a top secret experiment at a classified research center in the Lantaru sector. Research showed a single molecule of Omega contained the same power as a warp core, so theoretically a small chain could sustain a civilization indefinitely. Ketteract's goal was, according to Kathryn Janeway, an inexhaustible power source, though Seven of Nine pointed out its potential use as a weapon. Federation cosmologists theorized that the Omega molecule once existed in nature for an infinitesimal period of time at the exact moment of the big bang; some even claimed Omega was the the primal source of energy for the Big Bang.
The scientists were able to synthesize a single Omega molecule, which only remained stable for a fraction of a second. Upon its nearly instant destabilization, the research center was destroyed, killing all 127 scientists. An unexpected secondary effect [discovered by rescue teams en route] was the rupture of subspace within a radius of several light years, causing warp travel to become a permanent impossibility within this area. Starfleet Command realized the terrible implications: a chain reaction involving a handful of Omega molecules could devastate subspace throughout an entire quadrant, effectively ending interstellar travel for spacefaring civilizations in the quadrant.
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 enacted the Omega Directive in response to the Lantaru incident, 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, the captain would give the computer the proper high-level security authorization code to access the sensor data.
- The computer would then brief the captain regarding the detection of Omega molecules, followed by instructions to implement the Omega Directive at once – disregarding all other priorities, including the Prime Directive.
- The captain, absolutely forbidden from discussing anything about what was happening with any member of the crew, would contact Starfleet Command via an encrypted channel to inform them of the situation. Starfleet Command would then dispatch 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 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 both the molecule's existence (due to the Borg's own Omega experiments) and the Omega Directive (the Borg having assimilated Starfleet captains, thus their knowledge). Unable to call for an Omega team to deal with the problem, and after reluctantly considering First Officer Chakotay's counsel, Janeway therefore modified the protocols to their unique situation by briefing her senior staff [including Seven] on the directive, effectively enlisting the crew 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.
The Section 31 novel Cloak details the events that lead to the creation of the Omega Directive. In it, the USS Enterprise forces the USS Sphinx out of warp, having been sabotaged by Section 31 in order to prevent them from revealing the research station in the Lantaru sector. This leads to an investigation that reveals Ketteract's experiment to James T. Kirk and the crew of the original Enterprise. Although Kirk tries to appeal to Ketteract to stop the experiment, he is unsuccessful and the events described in "The Omega Directive" come to fruition.
In the game Star Trek Online mission "Sphere of Influence", the player character and major characters from the Federation and Klingon sides are taken by surprise when the character Commander Winters tells everyone that "all the monitors on the bridge are showing an Omega, we're locked out of the computers and the engine's off-line" after the Enterprise-F scanned what was on the other side of the Iconian gateway near Jouret IV, thus setting the stage for the Season 8 expansion.