While on an away mission, Janeway and Chakotay are bitten and become infected with a disease that the doctor can't cure. Something about the planet prevents the infection from hugging the two, but they are force to remain there if they are to survive. Voyager is forced to continue their trip home without the them.
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.