Stranded by the Kazon on a desolate planet ravaged by earthquakes and vicious cave creatures, the crew seeks food and shelter. At the same time, Paris, who managed to flee Voyager in a shuttle before the Kazon seized the ship, solicits help from the Talaxians.
On Voyager, the Doctor surprises Seska when he reveals that her newborn baby isn't Chakotay's child after all — he's Culluh's. After she leaves, the Doctor discovers that he's not the only member of the crew left on the ship; Ensign Suder, the violent sociopath whom Tuvok has been attempting to rehabilitate, is still aboard. They join forces against the Kazon, but as they plot strategy, Suder expresses regret over the fact that he will probably need to kill Kazon to wrest control of Voyager.
On the planet, Kes and Neelix are kidnapped by the primitive humanoid natives. Chakotay and a rescue party free them, but during their getaway, they're all forced to take cover in one of the dangerous caves. They manage to elude the enormous eel-like creature that lives inside, and seal off the opening as they exit.
As Paris heads back to Voyager with reinforcements, he sends a message to the Doctor, asking him to disable the secondary phaser couplings. Suder has been sabotaging Voyager's systems from within, using an old Maquis trick to avoid detection. But former Maquis Seska figures out that there's a saboteur aboard and confronts the Doctor. He claims that he's the only saboteur and Seska disables his program before he can disable the back-up couplings. That leaves Suder as the crew's last hope, and he heroically disables the phasers before being killed by a Kazon.
Paris knocks out Voyager's main phasers, and when Culluh tries to use the back-up system, Seska and many of the others on the Bridge are mortally wounded. She dies as Paris and the Talaxians board Voyager, and Culluh takes the baby with him when he abandons the ship. Paris takes control of the starship and goes back for the crew. Later, Tuvok offers a Vulcan prayer of peace over Suder's body as Janeway sets a course for home.