Voyager finds an alien junkyard and trades for supplies with the junk-dealer, Abaddon. Tom Paris discovers a rusty old shuttle in the yard and convinces his superiors to let him bring it aboard and restore it, just as he has been doing with old cars on the holodeck as a hobby. He discovers that the shuttle is equipped with a neural interface. It reads and communicates directly with its pilot's mind, giving it instantaneous maneuverability. He tries out the interface, and the ship makes a record of his brain patterns.
As time goes on Tom becomes more and more obsessive about restoring and caring for his new shuttle, which he has named Alice. He can even hear "her" speaking to him in his mind. His behavior becomes more and more strange. He wants to spend time with Alice and no one else, even his girlfriend, B'Elanna Torres, who is distressed about Tom's obsession. He begins to neglect his appearance and duties looking more tired and frantic as time goes on, and he wears a spacesuit designed for use with Alice instead of his Voyager uniform. When power cells from Voyager's back-up systems go missing, B'Elanna finds them in the cargo bay where Tom fixes Alice. She then sneaks aboard Alice to see what's drawing Tom there so strongly, but the ship springs to life, traps her inside, and shuts off life support.
Tom gets B'Elanna out of the shuttle before she is seriously injured, but soon after that he loses control of his own behavior. He boards Alice and speeds away from Voyager with her. They head for a space anomaly called a particle fountain. Alice inexplicably calls the fountain 'home'. Captain Janeway realizes they cannot fire on Alice because Tom is neurally linked to her and damage to the ship would kill him. B'Elanna taps into the neural interface from Voyager and speaks to Tom, her voice appearing in his thoughts alongside that of Alice. She pleads with him to hang on to her instead of the shuttle. Tuvok is able to sever the neural link between Tom and Alice, and the crew beams him away just as the shuttle is destroyed in the particle fountain.