After Chakotay and Janeway crash-land their shuttlecraft on a planet, Chakotay guesses they may have been shot down by Vidiians. Sure enough, a group of Vidiians arrives and attacks the pair, killing them. Suddenly, they're back on the shuttlecraft, under attack by Vidiian warships. The shuttle explodes before it can land. Seconds later, they are once again sitting in their shuttle.
Believing they're trapped in a time loop, the two officers contact Voyager and elude the Vidiians. However, back on the ship, Chakotay refutes Janeway's claims about the time loop. The Doctor diagnoses Janeway as suffering from the Vidiian phage disease and euthanizes her against her will, after which Janeway finds herself back on the shuttle with Chakotay. As they near a strange phenomenon in space, the shuttle explodes, and the next thing Janeway knows, she's back on the planet, watching Chakotay grieve over her dead body.
Returning to Voyager with Chakotay, Janeway discovers she cannot be seen. In Sickbay, the Doctor's attempts to revive her "corpse" are unsuccessful, but Janeway is able to get Kes to telepathically sense her presence. As the crew wonders if the Captain is lost in an alternate dimension, Janeway is shocked to come face to face with her deceased father. Admiral Janeway tells her that she really did die in the shuttle crash, and tries to convince her she should give in to death. Meanwhile, after days of unsuccessfully trying to reach Janeway, the crew holds a memorial service.
Janeway tells her father that she's not ready to leave the crew yet. Suddenly, she senses that she's still in her corporeal body, and that the Doctor is trying to save her. Her father tells her it's a hallucination and urges her to give up. Janeway knows her real father wouldn't push her in this way, and realizes that an alien has assumed his image to lure her to her death. Indeed, an alien presence has invaded her cerebral cortex, but now that she's aware of it, Janeway regains consciousness on the planet's surface, where she's recovering from injuries sustained during the crash-landing with Chakotay.