Voyager's route through the Delta Quadrant is tracked by Voth scientist Dr Gegen, with Hanon IV and the Nekrit Supply Depot among the locations ([#42 and #43 Basics] and [#55 Fair Trade] respectively). Gegen is in search of evidence about the true origins of his race who are a saurian species that he suspects evolved in a distant part of the galaxy, although the distant origin theory contradicts the doctrine of the powerful Voth elders. Gegen and his assistant Veer eventually find and board Voyager, at first undetected but then Voyager's sensors disclose the use of the Voth cloaking technology and the crew find Gegen and Veer. Gegen manages to escape, transporting back to his vessel with the unconscious Chakotay. Separately, the Doctor and Gegen discover that the Voth evolved from Earth's dinosaurs, avoided extinction, developed spacefaring technology and left Earth. When Gegen is charged with heresy by the Voth elders, Chakotay is the living proof of Gegen's theories. But before he can take Chakotay to his supporters, Voyager is transported inside a massive Voth city-ship and the crew detained. Defiantly Gegen agrees to face heresy charges, but retracts his theory when the Voth chairing the hearing threatens to destroy Voyager and send the crew to a detention colony.

Long-range scans indicate that if Voyager maintains its present course, it will enter a region of heavy tetryon radiation within two days. The alternative is a three-month detour.

The crew can access the manual overrides from main engineering to restart the ship's systems.

Tuvok erects a level 10 containment field around the bridge which prevents the Voth scientists from beaming off the ship, but they manage to beam to the messhall.

Starfleet uniforms contain a microscopic identification code indicating the name of the ship the crewman is stationed on.

microscopic identification code displayed via Voth equipment

Voyager is captured by a Voth city-ship and its systems come under Voth control.

Voyager captive within a vast Voth city-ship