A xenophobic alien race attack Paris and Torres while they are on a shuttle mission. This alien race is known for attacking intruders entering what they consider their territory. The aliens surprise Torres and Paris by beaming aboard the shuttle and knocking them unconscious with a strange weapon. The Aliens leave and Torres awakens and gets the still unconscious Paris back to Voyager.
Janeway decides to proceed ahead as no one in the system knows the boundary of the alien's space. The Doctor can't determine how to help Paris recover from the strange weapons effect. The Doctor is also feeling the effects his program being run beyond its design. The crew must fight the aliens through their space, while restoring the Doctor's program in order to save Paris from passing.
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.