A two-hour pilot episode sees a Marquis ship disappearing into the Badlands during some plasma storms. Captain Janeway at the helm of U.S.S. Voyager is assigned to investigate their disappearance. Understanding the Badlands as being a turbulent part of space that required the skill of a top-notch pilot, she seeks to recruit a convict who was an ex-Starfleet and a mercenary for the Maquis. With his help, Captain Janeway and the crew goes looking at the renegrades last known position in the Badlands.

However, Voyager is then mysteriously propelled 70,000 light-years from home by an overwhelming force. Searching this uncharted quadrant of the galaxy, they become embroiled in a centuries old environmental problem on a nearby inhabited world.