Voyager is suddenly rocked by a distant explosion. Although ship systems appear undamaged, all information and control screens are suddenly locked out and replaced by an eerie omega symbol. Captain Janeway arrives on the bridge and informs the crew not to worry. She orders the ship's computer to override and transfer all data to her ready room, but leaves without explaining to her bemused crew what happened. After locking herself in her office she asks the computer to brief her on the detection of "Omega". Janeway also summons Seven of Nine into her ready room, as the Borg also have their own knowledge of "Omega".
Because Voyager has been separated from Starfleet, the Omega Team (a specially trained group which would normally be tasked with handling situations involving "Omega") cannot be brought in to deal with the problem. Janeway decides to break the code of silence involving the symbol and share information with her senior officers. She announces that she has just received the Omega Directive, an order that requires Starfleet captains to ignore the Prime Directive and destroy the Omega particle at all costs. Omega is very unstable and even the destruction of one particle can nullify subspace for many light years around it, rendering faster-than-light travel impossible. Moving to the coordinates of the explosion they encounter the alien race that created it. The society is on the brink of economic failure, and are making Omega to "give their children a chance at a future." Seven of Nine, an ex-Borg member of the crew, displays an interest in the scientists' methods, hoping to save the omega particles and harness them, because she believes them to be perfection - infinite parts working together as one (like the Borg) - despite ample Starfleet and Borg evidence of their danger. The Borg are expected to assimilate it at all costs, even though they have experienced the loss of a large quantity of Borg vessels to Omega explosions while trying to harness the power of the substance. Seven notes, however, that the ability to harness Omega would make the Borg an unstoppable force; this remark only motivates Janeway to wipe out all omega particles, at any cost.
Eventually all the particles are safely gathered together and detonated a safe distance from the alien planet. Just before they are destroyed, they stabilize, and Seven is able to view perfection for a brief moment.