A strange reading appears on Voyager's scans. Janeway begins giving orders without explanation as she carries out the highly classified mission called the Omega Directive. Even though she is thousands of light-years from Starfleet, she is forbidden to explain although she confides in Seven who knows about it because the Borg Collective know. But when Chakotay dissuades Janeway from a likely suicide mission to destroy Omega, Janeway briefs the senior staff and a more workable plan is evolved.

Responding to the threat of Omega discovered nearby, (while still unaware of the nature of Omega), Torres is ordered to install multiphasic shielding around the warp core, and Paris is ordered to modify a shuttlecraft to withstand extreme thermal stress of at least 12,000 Kelvins.

Janeway's original plan calls for a gravimetric torpedo to be used to destroy the molecule. Seven constructs a harmonic resonance chamber based on the Borg design to contain and stabilise Omega. Since the torpedo would be insufficient to destroy Omega she modifies the chamber to emit an inverse frequency to dissolve Omega's interatomic bonds. In the end, a combination of both solutions are used.

the harmonic resonance chamber a second before it is sent into space

Janeway reveals to Chakotay: "The Omega Directive doesn't allow me to say much, but I want you to know what to expect. 0600 hours, I'll be leaving in a shuttle with Seven. ... One of two things is going to happen. Either Seven and I will succeed on our mission and return within a few days, or your long-range sensors will detect a large explosion in subspace. If that occurs, you'll have less than ten seconds to jump to warp and get the hell out of here. Head for the Alpha Quadrant and don't look back." Chakotay persuades her to abandon the shuttlecraft plan so no shuttlecraft is used.

Voyager is shaken by weapons fire from ships of Allos' people, and Seven notes that: "Any damage to our power grid could overload the chamber. Omega will chain react!" However, Voyager manages to eject and destroy the molecules before Voyager is damaged.

Until the briefing by Janeway of Voyager's senior staff (pictured), only starship captains and Federation flag officers have been briefed on the nature of the threat posed by the Omega molecule which is the most powerful substance known to exist. A single Omega molecule contains the same energy as a warp core. The molecule was first synthesised over a hundred years ago by a Starfleet physicist named Ketteract who was hoping to develop either an inexhaustible power source or a weapon. Ketteract managed to synthesise a single molecule particle of Omega, but it existed for only a fraction of a second before it destabilised and destroyed a classified research centre in the Lantaru Sector. Ketteract and 126 of the Federation's leading scientists were lost in the accident. Rescue teams attempting to reach the site discovered an unexpected secondary effect - subspace ruptures extending out several lightyears which make it impossible to create a stable warp field in the Lantaru Sector, and ships can travel through it only at sublight speed. The general public was allowed to believe this to be a natural phenomenon. As Omega destroys the fabric of subspace, a chain reaction involving a handful of molecules could devastate subspace throughout an entire quadrant and make warp travel impossible. When Starfleet realised Omega's power, they suppressed all knowledge of it.

Janeway orders the Doctor to prepare twenty milligrams of arithrazine, which is used for the most severe cases of theta-radiation poisoning. The Doctor insists that a physician must be present to monitor the treatment and it is against Starfleet medical protocols to provide that much arithrazine.