When Voyager happens upon a junkyard of old ships, the crew stops to purchase some parts from Abaddon, the salesman. Tom Paris falls in love with a small shuttle he finds among the junked vessels, and convinces Chakotay to let him restore it. He discovers the shuttle has a neurogenic interface, allowing it to interact directly with the pilot's thoughts. Tom gets to work immediately, naming his new toy "Alice." After a brief trial of the interfacing technology, Tom calls it a night. When he leaves, Alice powers on by herself, scanning Tom's brain imprint. In his quarters, Tom hears a female voice calling for him.
Driven by Alice's seductive power, Tom works nonstop on the shuttle. He and B'Elanna Torres try to celebrate its christening together, but Tom is obsessed to the point of excluding everyone. Tapping into Alice's database, he has found the flight suit design of her last pilot and is now wearing it instead of his Starfleet uniform. When Chakotay orders him to put his test flight on hold and attend to his official duties, Tom complains to Alice, whom he is now imagining as a flesh-and-blood woman. She eggs him on, convincing him to use the neurogenic interface again.
Alice goads Tom into stealing power cells from Voyager. When Alice traps B'Elanna, sealing a hatch and shutting off life support systems, Tom realizes the neurogenic interface is out of control. He rescues B'Elanna and tries to alert sickbay, but Alice won't let him. She forces him to launch the shuttle and complete the interface, making him one with the machine. As Captain Janeway and the crew realize what is happening, Tom fires on Voyager and escapes into warp.
The Voyager crew turns to Abaddon for answers. He explains that the shuttle Tom acquired is "haunted." Before he can say more, he begins hallucinating himself and suffers a cerebral hemorrhage. After receiving a cortical suppressant, Abaddon reveals that he too was once linked with Alice. She was looking for a top biological entity with which to work together in tandem, to guide her to an unknown point in space. After reconstructing data Tom left behind, Seven of Nine discovers where he and Alice are heading. They are going to an anomaly called a particle fountain.
Because Tom's synaptic functions are linked to the shuttle, Janeway cannot fire on him. Instead, Tuvok works to access the main computer and transmit a shutdown sequence. B'Elanna taps into his interface using a communication signal. With both B'Elanna's and Alice's voices in his head, Tom cannot think straight. Just as he is about to suffer a cerebral hemorrhage, Tuvok succeeds in shutting down Alice. Tom is beamed safely to sickbay, and Alice is destroyed in the particle fountain.