Lt. Paris and Ensign Kim are arrested and convicted of being part of a terrorist bombing. They are sent to an unusual prison located at the bottom of a long chute. To make matters worse, the prisoners are forced to wear a neck collar that affects their nervous systems.
Janeway, knowing Paris and Kim are innocent, set out to find the real bombers and free the two. Janeway is shocked to find, that when they capture the true bombers, this will not help her imprisoned crewmen. She then decides to take matters into her own hands.
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.