Voyager answers a distress call, only to find a bio-neural device imbedded in rock on a planet. Voyager beams the device back to Voyager, but then learns from the Doctor that the device is actually a weapon of mass destruction. Torres must remove the bio-neural mind of the device from the weapon. However, her attempt awakens it, and it then arms itself. Torres then tries to fry the device with an electro-magnetic pulse, only to find the device has taken over the Doctor's program. Now the device / Doctor demands it be taken to its intended target, the home planet its creator's were at war with.
Every attempt to deceive the device fails, and soon Voyager finds itself surrounded by thirty-two more devices. Voyager must now stop all the devices from completing their task, as Voyager's investigation reveals that the devices had been given a recall order, as the war is over; an order the devices refused to accept as being a deception by the enemy.
While chasing a renegade Maquis ship in the Badlands, the USS Voyager and the Maquis ship they are chasing are pulled into a vortex, which sends them instantly to the Delta Quadrant. However, after the destruction of the device that transported them to the Delta Quadrant, the crew of Voyager and the crew of the Maquis ship must join together to fight their way back to their home in the Alpha quadrant, which is many years away. They will meet many foes and many obstacles along the way, but they will also bond as a crew, between those of the Maquis and those of Starfleet.