Janeway weighs destroying the Array that stranded her ship, while Voyager's crew faces a long road home.
The second half of the pilot reveals that the dying Caretaker has been pulling ships into the Delta Quadrant in search of a compatible being to take over his role as protector of the Ocampa. While Paris and Tuvok, guided by Kes, descend into the Ocampa's underground city to rescue Harry Kim and B'Elanna Torres, the Kazon attack the array, hoping to seize it.
Janeway decides to destroy the array so the Kazon cannot turn it against the Ocampa, knowing this ends any chance of a quick trip home. Chakotay sacrifices his Maquis ship to protect Voyager, and the two crews merge under Janeway's command with Chakotay as first officer, setting up the long journey that defines the series.