The crew continues to enjoy the Fair Haven holodeck program. After Lt. Tom Paris' suggestion, the holoprogram is set to run continuously, but over time, the strain put on the holotechnology begins to cause problems. The hologram characters begin to realise that the visitors are capable of changing the world at will (normally, holograms' programming makes them oblivious to non-in-world aspects). Scared by this the villagers begin to suspect that the crew is a group of spirit folk that came to destroy Fair Haven. Captain Janeway manages to elude her boyfriend, Michael the barkeeper, but nevertheless asks Tom and his friend Ensign Harry Kim to figure out the problems with the Fair Haven program. The two establish that the subroutines supposed to make the holograms unaware of things outside their program have malfunctioned due to prolonged operation. When Tom and Harry enter the program to fix it, however, they are captured and held hostage by the holograms, who begin to try to make Tom and Harry spill secrets about the spirit folks. The Doctor (who has been playing the role of a village priest) enters the holodeck using his mobile emitter (to avoid being influenced by the damaged holo-program) but is soon deprived of it and tied with Tom and Harry. Michael, determined to find his girlfriend, puts the emitter on. Janeway, thinking that it's the Doctor who's wearing it, orders that he be transported to the bridge. At this point, Janeway can no longer (completely) deceive Michael. She explains to him that her crew are on a spaceship on a long journey, and that they enjoy the occasional visit to peaceful Fair Haven. They afterwards reenter the holodeck and convince the other characters that the crew had no hostile intentions.
This story arc is begun in the previous Season Six episode of Fair Haven the other Voyager episode featuring the town.