A Starfleet directive known only to captains and flag officers, ordering the destruction of any Omega molecules found and suspending every other rule, including the Prime Directive.
The Omega Directive is among Starfleet's most closely kept orders. It was written after a 23rd-century experiment showed that a single unstable Omega molecule can destroy subspace across a wide region and make warp travel there impossible. Only starship captains and flag officers are told of it, and it requires them to destroy Omega wherever it is found, at any cost.
In the Voyager episode The Omega Directive, the ship's sensors detect the molecule. The computer drops the ship out of warp, fills every screen with the Greek letter and locks out all but the captain. Janeway, far from the specialist team that would normally take over, has to tell her senior staff what is going on.
She states that the Prime Directive does not apply for the length of the mission. Seven of Nine, who knows Omega from the Borg and regards it as perfection, helps build the chamber that destroys the molecules.