The episode starts with a battle between the Maquis and the Cardassians - the Maquis being people formerly associated with the United Federation of Planets living in space now ceded to the Cardassians as part of a peace treaty. A bizarre space phenomenon seems to destroy the Maquis ship.
Janeway makes a trip to a prison on Earth, to get Tom Paris to agree to be released; on condition that he act as an advisor to help catch his former friends in the Maquis. He agrees, and is taken to the Starship Voyager; at Deep Space Nine. Whilst at the station; we meet Quark who attempts to fleece a young member of the crew, Harry Kim.
The Voyager soon departs, and is swept up by the same type of phenomenon that got the Maquis ship. It is discovered both ships have been transported to a site in the Delta Quadrant; near an array. A member of each crew, Harry Kim, and B'Elanna Torres, have been abducted. It is discovered that the entity responsible for bringing them their is the dying Caretaker of a nearby world. This world, peopled by the Ocampa, was nearly destroyed by his people ages ago, and he has remained there to look after them.
The Voyager crew ultimately free the Ocampa from their closed-off underground facility, and destroy the Array to stop the Kazon, their enemies from being able to use it. As a side-effect of this, they trap themselves in the Delta Quadrant. The Maquis crew is integrated into the Voyager crew (they had lost about half in the accident), and the ship sets out to make the estimated 70-year voyage to Earth.