4. In the Flesh

On stardate 52136.4, the Federation starship Voyager encounters a space station that contains a near-complete recreation of Starfleet Academy on Earth. First Officer Chakotay and Tactical Officer Tuvok have investigated the recreation, finding that those inside appear to be Starfleet personnel, cadets, and others, such as the groundskeeper Boothby, played by Ray Walston. Chakotay also meets an officer, Commander Valerie Archer, and arranges to meet her later for a date. Caught in an area they should not be in by a cadet, Chakotay and Tuvok stun him and transport him back to Voyager.

When they attempt to question the cadet and take a DNA sample, he commits suicide. The Doctor discovers the "cadet" is really a genetically-altered member of Species 8472, a highly dangerous race the crew had previously encountered. Captain Janeway orders Seven of Nine to begin preparing warheads using her Borg nanoprobes, but also looks for a diplomatic solution, sending Chakotay back to the simulation to learn more.

Chakotay keeps a date he earlier arranged with Valerie, during which she speaks candidly about the simulation, with which Chakotay attempts to play along. Valerie secretly takes a sample of his DNA and discovers that Chakotay is human. She alerts her superiors, and soon Chakotay is captured. Boothby, appearing as the highest-ranking member of Species 8472 present at the simulation, interrogates Chakotay, believing that Starfleet is preparing to invade fluidic space and attack their species. The Voyager crew arrives at the simulation to attempt to rescue Chakotay, creating a tense stalemate. Janeway and Boothby agree to enter negotiations to settle the matter peacefully.

During these talks, the Voyager crew learn that this station is but one of several similar training grounds for Species 8472, and question if the species themselves are planning to invade Earth, while the aliens steadfastly refuse to believe that Starfleet is not preparing to attack them. Janeway, seeing the stalemate, orders her crew to stand down, which gains the trust of Valerie and Boothby. They reveal the stations are not a staging area, but only a reconnaissance mission to prepare themselves for an eventual invasion by Starfleet. Agreeing that a truce is possible, the Voyager crew trades information on the Borg nanoprobes for Species 8472's information on genetic modifications. The two sides complete their discussions, and soon Voyager resumes its journey home with less fear of the threat from Species 8472.