Lieutenant Paris (now Junior Grade, evinced by the partially filled pip on his collar), Chief Engineer Torres and Ensign Durst fail to return from an away mission to a planet. 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. Commander Chakotay takes a team to investigate and discovers 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 human version of Torres, meanwhile, is kept imprisoned with Paris and Durst. The Vidiian scientist studying Klingon Torres sees her going through the first symptom of severe agony, but she is fighting off the disease. Meanwhile, Paris, still in the holding cells, finds B'Elanna as a full human. While there, B'Elanna explains her origins, of how her father left when she was five and how she did everything to hide her Klingon heritage as a child. Klingon B'Elanna tries to use her feminine charm to have the scientist release her, but his desire to find a cure overrules his lust. In the holding cells, two guards arrive and take Ensign Durst. The human B'Elanna is scared as opposed to her Klingon half's relentless tenacity. After reviewing what they know from the last time the Vidiians encountered Voyager, the crew begin running simulations on how to get past the Vidiian force fields. In a naive effort to calm his prisoner, the Vidiian scientist kills Durst and uses his face to cover his Phage-ravaged features to try to better impress Klingon B'Elanna.
However, the scientist has underestimated Klingon strength and the Klingon Torres breaks free from her restraints and escapes the laboratory. The senior staff on Voyager come up with a possible way past the force field by transporting through a micro fissure. To prevent capture, Chakotay disguises himself as a Vidiian. In her efforts to escape the complex, Klingon Torres finds her human counter-part. After finding some food, and common ground, the two halves 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, meets up with Paris, and locates the group in a control room, holding the Vidiian scientist at gun-point. Just as the human Torres is about to disable the shields, the alarm sounds, the scientist arrives and fires at her, but the Klingon Torres takes the shot and is killed, destroying the potential cure for the Phage. The group escape back to the ship. Back on Voyager, the Doctor explains that he can restore the human Torres to her original self by re-integrating the Klingon DNA over the course of several days and that he must because without her Klingon half, Torres would die. Human Torres admits that although she admires her Klingon half, once re-integrated, she realizes that she'll spend the rest of her life fighting within herself.
Dawson's initial reaction to the script of "Faces" was one of doubt; she felt that it occurred too early in the series and that she did not know the character well enough to play her as two separate people. But she used the episode as a learning experience and learned more about her character, and in turn it became one of her favorite episodes. After the episode aired, she called her parents to ask their opinions, and they replied, "You were good, but the girl that played that Klingon was really great!", which Dawson took as a compliment.