While on a short-term mission to track an infiltrated Maquis cell, Capt. Kathryn Janeway and her newly launched U.S.S. Voyager crew -- and the Maquis fighter crew -- are drawn 70,000 lightyears to the far side of the Delta Quadrant by an alien seeking survival, calling itself "the Caretaker." As the Voyager and Maquis crews forge a tentative bond of survival, Janeway decides to cut off the escape route homeward to deal with the aggressive Kazon-Ogla, the Ocampa's devastated world, and the "Caretaker" who blames himself for it.

The reality of co-existence hits Maquis and Starfleet personnel alike, but the troubled but brilliant B'Elanna Torres is made chief engineer after solving a baffling spatial mystery with Janeway.

An industrial but pre-warp planet's dangerous polaron technology seems to be the cause of a planet-wide wipeout discovered by the Voyager crew -- or did the visitors actually cause the problem in the near past?

When a grotesque and bizarre alien team steals Neelix's lungs, the Doctor's holographic replacements keep him alive until Janeway finally tracks down the Vidiians and their society-wide Phage plague.

A nebula whose baffling interior provides no exit while being explored is discovered to be a living entity, and Janeway leads the crew in delicate "surgery" to repair the damage and finally emerge intact.

The crew is overjoyed to find a wormhole leading to the Alpha Quadrant, only to find that it is micro-sized and terminates in the Romulan Empire. The lone Romulan they contact, however, eventually seems won over to helping them.