Stardate 51871.2: When the large Greek letter omega appears on Voyager's bridge displays, Captain Janeway locks herself up in the ready room and commits herself to a strange and strictly secret procedure. The Omega Molecule, a very powerful but highly unstable substance, has been detected by the ship's sensors, and it is a Starfleet captain's foremost duty to destroy it at all cost before it can disrupt subspace. She initially only lets Seven of Nine in on what she is doing, considering that Seven has the knowledge of assimilated Starfleet captains. But when Janeway plans to go on a shuttle mission that could kill her, Chakotay advises her to rely on the capabilities of her ship and crew. Voyager finds a destroyed research outpost on a moon. After rescuing the survivors, Janeway investigates the remaining Omega Molecules. There are too many to simply destroy them with a detonation, so Janeway goes with Seven's suggestion to use a harmonic chamber. Harnessing the Omega Molecules is an old obsession of the Borg, so Seven makes every effort to persuade the captain not to destroy them, but Janeway orders to carry on with the procedure. When alien ships follow Voyager to retrieve the molecules, Janeway decides to decompress the cargo bay with the harmonic chamber and destroy the rest with a photon torpedo. Only seconds before the decompression, the molecules eventually stabilize, but it is already too late to preserve them.

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