Voyager answers a distress call and finds an artificial intelligence lifeform apparently suffering a technical form of amnesia, and it is beamed aboard Voyager for repair only for it to commandeer the Doctor's program and recall that it is actually a weapon of mass destruction set for a target it never reached. Speaking through the Doctor's body, the machine tells Janeway that she must help it find its target, or it will destroy Voyager. After Janeway is given new co-ordinates to follow, Neelix locates a merchant who wants to obtain the weapon. But when the merchant tries to get transport the machine, it sends an antimatter surge back through the transporter beam and destroys him and his ship.

Seven realises her Borg nanoprobes can be adapted to disable the weapon's circuitry. The crew devise a plan. They reconfigure Voyager's sensor array to send false telemetry to give the impression they are navigating a minefield, with Paris planning to simulate mine explosions with carefully timed disruptions to the inertial dampers. To similate a a large explosion Janeway orders the plasma relays on Deck 6 to be blown out. Seven will be brought into sickbay pretending to suffer from burns, and Tuvok will disrupt the Doctor's program. The plan will give Seven time to inject her nanoprobes into the weapon and disable it.

Meanwhile, Kim and Torres retrieve lost data from the weapon's memory files, which reveal its launch was a mistake. The machine thinks they are deceiving it and refuses to abort. Suddenly Voyager is suddenly surrounded by thirty-two similar weapons which order the machine to transport from Voyager to the target. However, Kim persuades it to look for his people's confirmation code in the rest of its memory files. It does so and confirms the order to cease his mission was valid. But when it tells the other weapons to stand down they cannot be diverted. The weapon then reconfigures its bio-neural matrix and joins the others. Ite leads them to a safe distance, then detonates, destroying them and itself too.

According to the Officer's Manual, Section 126: "When taken captive by a hostile alien force, seek an opportunity to engage the assailant."