The United Federation of Planets's top researchers in the field were killed in an Omega explosion; apparently, the particle is extremely unstable and attempts by the Federation to harness its power failed. A side effect of the Omega explosion is the disruption of subspace, leaving the area of space incapable of sustaining a warp field.
When the Federation realized the dangers of the particle, they created a directive aimed at destroying Omega, thereby preventing any chance of Omega exploding. The directive supersedes the Prime Directive and only captains and admirals are aware of the directive.
Captain Kathryn Janeway of Voyager encountered a large concentration of artificially created Omega molecules in the Delta Quadrant and was able to destroy Omega.