An Omega molecule is a highly unstable molecule and the most powerful substance known to exist. The Borg knew it as Particle 010. The molecule could be synthesized with sufficient amounts of boronite ore. However, proper containment methods did not exist to prevent the violent destabilization of the molecule, which destroyed subspace and rendered warp travel impossible. The explosion of one molecule could destroy all subspace within several light years.

A single Omega molecule was synthesized in the late 23rd century by the Starfleet physicist Ketteract on board a classified research station in the Lantaru sector. The molecule remained stable for a fraction of a second before it exploded, killing Ketteract and one hundred twenty-six other leading Federation scientists. Additionally, an unexpected secondary effect was the creation of a subspace rupture extending out several light years. This made it impossible to create a stable warp field, complicating rescue efforts.

After the accident was covered up, Starfleet suppressed all knowledge from the general public, and the impassibility of the Lantaru sector was falsely attributed as a natural phenomenon. By the late 24th century, Starfleet had come to the conclusion that Omega molecules represented a threat not only to the Federation, but to the entire galaxy. A chain reaction involving a handful of molecules could devastate subspace throughout an entire quadrant. If that were to happen, subspace capabilities like Warp drive and subspace communications would be rendered impossible. Without faster-than-light travel or interstellar communication, space-faring civilization would cease to exist.

Starfleet suppressed all knowledge of Omega and authored the Omega Directive, on which only starship captains and flag officers were briefed. Specialized teams could be dispatched to deal with Omega-related crises. All priorities and protocols, Starfleet Medical protocols and even the Prime Directive could be suspended during these missions.