Holograms in Fair Haven become self-aware.
At Tom Paris's urging the Fair Haven holodeck program is left running continuously, and the strain breaks down the subroutines that keep its characters unaware of their artificial world. The villagers notice the visitors changing their surroundings and decide that the crew must be spirit folk bent on destroying the town.
When Paris and Kim try to fix the program, the villagers capture them, and they also seize the Doctor, who visits in the role of the local priest. Michael Sullivan, Janeway's holographic romance, ends up on the bridge wearing the Doctor's mobile emitter, and Janeway tells him the truth. The crew persuades the villagers they mean no harm, and Torres repairs the program.