The crew tracks a Cardassian-designed weapon packing a warhead capable of wreaking mass destruction. While serving in the Maquis, Chakotay and Torres encountered the missile, dubbed "Dreadnought," in the Alpha Quadrant. Back then, Torres had reprogrammed it to assault its own makers, but the weapon went astray and was thought to have been destroyed. Now Voyager's scanners report that Dreadnought is inexplicably headed straight for a heavily populated planet in the Delta Quadrant.
As Jonas, a traitor in Voyager's crew, informs the Kazon about this superweapon, Janeway warns an official on the planet Rakosa about the approaching missile. Torres beams onto Dreadnought, where she gets the device's sophisticated computer system to stand down from its attack plans. But a short time later, Torres learns that Dreadnought has inexplicably resumed its deadly course for Rakosa.
The crew learns that Dreadnought's computer does not "believe" it's in the Delta Quadrant. It thinks Rakosa is actually a Cardassian target in the Alpha Quadrant, and that Torres has been coerced by the Cardassians into logging false information into its navigational sensor array. Attempts to disable the missile from Voyager backfire when Dreadnought blows out many of the starship's main systems.
With two million lives at stake on Rakosa, Torres manages to beam back on Dreadnought as the Rakosan fleet approaches to intercept the missile. Under fierce fire from Dreadnought, however, the Rakosan ships retreat. As a last-ditch effort, Janeway orders her crew to abandon ship; she plans to use Voyager to ram the missile and detonate the warhead before it hits Rakosa.
Not a moment too soon, Torres manages to initiate an old Cardassian program in Dreadnought's systems. The two programs immediately begin to "quarrel" about the missile's target, distracting it from her attempts to breach Dreadnought's containment field and detonate the warhead. When Voyager's sensors convey Torres' success, Tuvok beams Torres back to the starship just as Dreadnought explodes.