The crew witnesses atypical behaviour of an inversion nebula and stop to study it. They watch as a plasma strand ignites but it fails to create the expected chain reaction throughout the nebula. Sensors show a dampening effect of unknown origin between the strands. When Voyager attempts to resume its course, the propulsion system inexplicably goes offline, requiring the engineering crew to try and diagnose the propulsion problem, Voyager's engineering team determines that the warp drive is functioning within established levels, matter/antimatter containment is at recommended field strength and the impulse engines are also within tolerance. This leads them to believe there is a computer malfunction, so they run a level 4 diagnostic. A team 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 where he meets Marayna, a lonely humanoid alien who controls the plasma activity for the benefit of her home world's inhabitants, and who had previously manifested herself to the Voyager crew as a holodeck character.

Voyager and the inversion nebula

There are crew quarters on Deck 3 as Kim's quarters are on that deck. By [#81 Waking Moments] his quarters have changed to Deck 6.

Holodeck controls on the holodeck (currently running Paxau Resort holoprogram).

holodeck controls

The ignited plasma strands result in inertial dampers going offline and a loss of shields. (See also STATUS REPORT.)

Chakotay notes that there is precedent for a hologram gaining sentience and taking over the ship. This refers to the Moriarty holocharacter in the Sherlock Holmes holoprogram on USS Enterprise NCC-1701-D. Events are depicted in [TNG: Ship in a Bottle]. Kim says that he learned about the incident at Starfleet Academy.