Lieutenant (Junior grade as evident by the now 2nd dot on his uniform being partially filled starting in this episode vs fully filled in previous episodes), Paris, Chief Engineer Torres and Ensign Durst fail to return from an away mission to a planet. Commander Chakotay takes a team to investigate and discover that the caves in which the away team were working have shifted. They deduce that the caves are illusions: advanced holography as used by the Vidiians in a previous encounter with the Voyager crew.
The away team have been captured by the Vidiians, and a Vidiian scientist has used advanced medical technology to create two forms of Torres from her mixed DNA, one pure Klingon and one pure human. The scientist hopes to create a cure for the Phage, a deadly disease that afflicts his entire race, by studying the unusual resistance that Klingon metabolism has to it. The human version of Torres, meanwhile, is kept imprisoned with Paris and Durst.
The Vidiian scientist, however, has underestimated Klingon strength and the Klingon Torres breaks free from her restraints and escapes the laboratory. In her efforts to escape the complex she finds her human counter-part, and the two work together to formulate a plan. The human Torres suggests finding a Vidiian computer console and shutting down the shields for the complex so that Voyager can transport them to the ship, while the Klingon Torres deals with guards they encounter on the way.
Meanwhile, Chakotay, disguised as a Vidiian guard, breaks into the facility and locates the group in a control room, holding a Vidiian guard at gunpoint. Just as the human Torres is about to disable the shields, the guard fires at her, but the Klingon Torres takes the shot and is killed. The group escape back to the ship.
With the group back on Voyager, the Doctor explains that he can, and must for health reasons, restore the human Torres to her original self by reintegrating the Klingon DNA.