Voyager receives a distress call from a small ship. When they make a lifescan of the vessel, they are surprised that the occupant is an Ocampa. They make contact with it, and the bridge crew is shocked to see Kes on the viewscreen, almost three years after she left the ship and was not heard from again. Now here she is, looking elderly, tired, and desperate. She begs permission to come aboard, which Captain Janeway eagerly grants. Instead of docking her ship, Kes accelerates, ramming Voyager hard enough to breach the hull. Before the impact she had beamed herself aboard, and has begun stalking the decks of the ship, blowing out entire walls with neurogenic energy and the force of uncharacteristic anger.
Blowing past security Kes enters Engineering. She connects herself physically to the warp core and begins to absorb power from it. When B'Elanna tries to intervene, Kes blasts her with energy, killing her instantly. Kes then disappears in a flash.
She materializes in an earlier time (2371). It's Voyager's first year in the Delta Quadrant and Kes assumes a younger appearance to blend in. She goes to the aeroponics bay, where she stuns and hides her younger self. Barely disguising her anger and hostility, she interacts with the crew when she must, taps into the communications system and plots a course for her home world, Ocampa.
Tuvok, who has psionic abilities similar to those of Kes, senses something amiss with her. He begins having strange hallucinations. He remembers the Delta Flyer three years before it was even built, and he has a vision of five-year-old Naomi Wildman, who has not yet been born. He follows the little girl into a cargo bay where he discovers Seven of Nine in a Borg regeneration alcove. He snaps back into his own time, puzzled.
Meanwhile, Kes makes a covert transmission to the Vidiians, who are currently in conflict with Voyager's crew. They seek the crew, hoping to capture them and harvest their organs and tissues. Kes promises to hand them over in exchange for passage back to Ocampa. She has no affection for her former crewmates, who she believes abandoned her.
Tuvok has more intense hallucinations and collapses. At the same moment The Doctor and Janeway detect a burst of tachyon particles in his vicinity, indicating temporal disturbances. His visions may actually be glimpses of the future.
Thanks to Kes' information, the Vidiians locate Voyager and attack. Janeway tracks down Kes' transmissions and goes after her. She finds Kes and her angry future counterpart, who lashes out at her. She cries that her life has been miserable since Janeway and crew encouraged her to develop her mental abilities. She feels she wasn't ready to leave the ship and wander the galaxy alone. For this she blames the Voyager crew and is determined to hurt them and rescue her younger, innocent self. She attacks Janeway, who is forced to kill her in self-defense. Voyager fights off the Vidiians, albeit with significant damage to the ship. The younger Kes, who has no idea what is going on, revives and assists Janeway and Tuvok. Kes creates a holographic message to give to her future self.
Three years later, Janeway and Tuvok remember the earlier encounter with Kes. When Kes appears and aims her ship at Voyager they prevent the collision, and then rush to Engineering, which has been safely evacuated. The furious elderly Kes has just been stopped in her tracks by the holographic recording of herself. The younger Kes gives her angry older self a message, imploring her to leave Voyager alone. When Janeway and Tuvok arrive, they talk her safely back to her undamaged ship, easing her anger, and wishing her well on her journey home.