Voyager has entered an area of space that is totally dark. The lack of stars outside the ship's windows has made the crew tense and depressed. They only feel worse when they find out that it will take Voyager two years to travel to the other end of "the void" at top speed. Everyone reacts in their own way; Neelix has panic attacks, Paris and Torres fight even more than usual, Harry spends his boring duty shifts practicing his clarinet, and the crew spends a lot of time in the holodeck.
No one has seen Captain Janeway in weeks. She has been spending the long, uneventful shifts in the dark void isolated in her quarters, seeing no visitors, just thinking of what has happened over the last four years. She still feels immense guilt for having made the choice that stranded Voyager in the Delta Quadrant. She notes that the crew is very unhappy right now and takes it personally.
One day, something knocks out all power on the ship. A field outside the ship is draining Voyager's systems, and there is total darkness. While the lights are out, aliens enter the ship. One of the intruders attacks Paris, but Seven of Nine is able to stun the alien. Janeway emerges from her quarters and helps her crew fight off the intruders. When they get the power back on they see that Voyager is surrounded by a fleet of small ships. A larger ship sweeps in and attacks them, and the aliens leave Voyager. The pilot of the larger ship, Emck, is from a people called the Malon. He promises to show Janeway a vortex that serves as a quick shortcut out of the void if she will turn over the injured alien to him. It is tempting but she refuses.
In sickbay the injured "night alien" apologizes for disabling Voyager and explains that his people are on the defense against the Malon, who are poisoning the area with theta radiation. The Malon specialize in transporting and dumping hazardous radioactive industrial waste, and since he has no respect for the local inhabitants, he has been dumping it in the void. The night alien begs Janeway for help.
Emck comes aboard Voyager to negotiate. Torres explains to him that the Malon could easily recycle the hazardous radiation and use it cleanly for energy, as they do on Voyager. They would not have to dump it at all. The Malon says it is a great idea except for one thing: he makes his living carrying and disposing of the waste. Turning to recycling would ruin the entire industry in which he makes his livelihood. Emck plans to happily continue dumping radiation in the night aliens' home.
Janeway knows she can destroy the vortex connecting the void to outside space. She could shut the Malon out of the void and save the night aliens. The problem is, it would also close Voyager's shortcut out of the dark expanse and they would have to endure it for two long years. Janeway does not want to be responsible for stranding her crew yet again. She agonizes over the decision and then assembles her senior staff to make an announcement. She will send Voyager through the vortex under Chakotay's command, while staying behind in a shuttle to destroy the vortex once her crew is safely through. The crew balks at this, flatly refusing to take Voyager on without the captain. She drops the idea, understanding that Chakotay had informed the crew beforehand that she would propose some sort of grand self-sacrifice for herself and that they should all unite in defiance. She realizes and accepts that the crew do not blame her or harbor resentment toward her personally for condemning Voyager to a lifetime in the Delta Quadrant.
A backup plan develops. They battle through the Malon front, enter the vortex, and blow the inner portal, riding the shock wave out the other end. The vortex is destroyed, the night aliens are safe from the Malon, and Voyager clears the void. Before them lies a welcome sight - millions of stars.