Voyager receives a distress call from a small vessel, piloted by a much older and weathered Kes. Captain Janeway grants her permission to come aboard, but she comes in much too fast and the vessel collides with Deck 9. However, Kes beams herself aboard Voyager just before impact.
A cold and angry Kes uses her psychokinetic abilities to disable the ship's systems, giving off high levels of neurogenic energy that destroy everything in her path. Even a forcefield and a phaser shot from a security guard cannot stop her as she carves a path of destruction toward Engineering. Torres and Seven of Nine, shocked to see that the invader is Kes, train weapons on her, but the phasers ripple and distort in their hands. Kes steps up to the warp core and places her hands upon it. Just as Torres goes to shut down the core, she is struck by a tendril of energy. Seven rushes over to Torres' dead body, while Kes vanishes in a flash of light.
When Kes disappears, she travels backward in time to Voyager as it was five years earlier, only a few weeks since being pulled into the Delta Quadrant. Sneaking up behind the original Kes, the undetected Kes from the future injects her with a hypospray, rendering her unconscious.
The Janeway of this time period is concerned that another conflict may soon ensue with the Vidiians since two more ships have been detected on long-range sensors. On a secure channel, Kes from the future makes contact with the Vidiian captain. She tells him she will provide him with information necessary to capture Voyager, in return for her safe passage home to Ocampa.
Meanwhile, Tuvok seems to be experiencing premonitions. Stepping into a turbolift, he encounters a young girl who identifies herself as Naomi Wildman. Tuvok follows the girl into the Cargo Bay, and when the doors open he sees Seven of Nine and the Borg children from the future regenerating in Borg alcoves.
The Doctor confirms for Captain Janeway that Ensign Wildman is expecting a baby girl. Back in Engineering, Tuvok is once again having visions of the future. This time he experiences a fragmented replay of events when Torres is struck in the back with an energy tendril as a much older Kes looks on. Tuvok is brought to Sickbay where he begins to convulse upon the surgical bed. Janeway views the proximity scan of Tuvok at the time he collapsed in Engineering, and discovers there was a surge of tachyon particles. Since tachyons are normally generated by temporal distortions, Janeway concludes there's some form of time travel involved.
When Janeway orders the bridge crew to scan for tachyon particles, Voyager suddenly finds itself under attack by the Vidiians. The crew realizes the Vidiians know more than they should about Voyager, including when they would be coming out of warp, their shield frequencies and which systems to target. Chakotay detects a transmission originating in the Airponics Bay, where he picks up two bio-readings that both read as Kes. Janeway heads to Airponics with a Security team as the bridge crew tries to break off the grappling hook that the Vidiian ship has attached to Voyager's hull. Meanwhile the Vidiians have started boarding Voyager, and Janeway must evade them in order to enter the Airponics Bay.
She makes it, and confronts the Kes from the future. Kes tells Janeway she wants to rescue her past self, that she was taken from her home and made a prisoner on the ship, corrupted with ideas of exploration and discovery. She accuses the Captain of encouraging her to develop her mental abilities before she was ready, and now she would not be able to return home to Ocampa because her people would be frightened of her. Kes attacks Janeway telekinetically, but meanwhile Voyager breaks free of the Vidiian ship, and the resulting jolt leaves Kes off balance. Eventually Janeway is able to blast the future Kes with a phaser and kill her. When the Kes of the past recovers, Janeway asks her help to prevent something terrible from happening in the future.
When an older Kes hails Voyager again in the future, the crew is already prepared. This time Captain Janeway orders the warp core shut down completely. When Kes enters Engineering, the Kes from the past appears in a message that she recorded to herself five years earlier. She reminds the older Kes that she made her own choices, and that the people she came back to harm care about her. Janeway approaches and reminds her why she made that recording. She urges her to stay on Voyager, but Kes says she needs to be with her own people. Finally she remembers making the holo-recording, and her anger dissipates. Realizing she can go home after all, she transports back to her vessel after a brief and awkward reunion with Neelix.