The crew is mystified by the atypical behavior of an inversion nebula. While they study it, Kim asks for Tuvok's help in suppressing his emotions. The ensign confesses he's fallen in love with a holodeck character named Marayna. Tuvok advises Kim to avoid further contact with her, since it is impossible to have a relationship with a computer subroutine. Kim agrees.
On the Bridge, the crew watches as a plasma strand ignites, but fails to create the expected chain reaction throughout the nebula. Sensors show an unknown dampening effect between the strands. That night, despite his vow to avoid Marayna, Kim accompanies Paris to the holodeck. There he sees Marayna in conversation with Tuvok. Troubled, Kim leaves, while Tuvok continues to talk to Marayna. The Vulcan is surprised at the depth of her insight into his nature, and he admits that he understands why Kim finds her so compelling.
When Voyager attempts to resume its course, the propulsion system inexplicably goes off-line. While the engineering group explores the problem, Kim goes to the holodeck and finds Tuvok again visiting Marayna. He accuses the Vulcan of betraying his trust, and Tuvok opts to delete Marayna's program rather than jeopardize his relationship with Kim. He's surprised, therefore, when he finds Marayna in his quarters.
To Marayna's annoyance, Tuvok calls security, but she disappears when they arrive. The crew investigates the holodeck and discovers that someone outside the ship has created an uplink and tapped into its programs. Suddenly, activity in the nebula increases, threatening the safety of the ship.
Tracing the uplink back to its source, Tuvok beams over to a space station located inside the nebula. There he meets the real Marayna, a lonely humanoid alien who controls the plasma activity for the benefit of her home world's inhabitants. She threatens to destroy Voyager if Tuvok doesn't stay with her, but he explains that their relationship would not be what she desires if he stayed only to save his ship. Accepting the logic of the situation, she allows him and Voyager to leave.