Upon encountering any evidence of the presence of Omega Particles, all federation captains must follow these commands:
- Report the detection to Starfleet Command immediately.
- Use any and all means available to destroy the Omega Particles immediately.
- Under no circumstances are any personnel of rank beneath Captain to be informed of the situation.
- This procedure is to be executed regardless of any other Starfleet policies and other considerations, including the Prime Directive.
The Omega Directive is a classified General Order binding upon all ships in service of the Starfleet of the United Federation of Planets in the Star Trek universe. It is most notable among the other General Orders for its specific supercession of the Prime Directive.
The Omega Directive was put into effect after the devastating results of an experiment conducted at a Federation research facility. In an attempt to produce an energy source that was unparalleled, scientists synthesized the Omega Particle, a substance theorized to have contained the energy that initiated the Big Bang1. The particle only remained stable for less than one second, exploding and destroying the base.
Unfortunately, that was the least of the problem
The explosion also trashed subspace for within 3.2 lightyears of the planet, rendering warp travel and FTL communications impossible. When Starfleet got wind of this, they initiated a massive cover-up of the incident and created the Omega Directive.
Fast-forward to 2374, and the only canon Omega Directive incident occurs aboard the U.S.S. Voyager in the Delta Quadrant. The ship detects the detonation of multiple particles less than ten lightyears away, and Janeway orders the ship in to carry out the Omega Directive. Because of their inability to contact Starfleet and call in a specialized team, Janeway is ultimately required to explain the situation to her senior staff. The particles are eventually destroyed in a resonance chamber and then by a gravimetric torpedo, but before their destruction, the particles are observed to stabilize.
- Why this wasn't a BIG RED FLAG we'll never know.