The episode opened with Chakotay observing a facility on a planet that appears to be a Starfleet training compound. He encountered a population of aliens who have assumed human form and created a simulation of Starfleet Academy. During his initial recon, Chakotay met the grounds-keeper, Boothby. The inhabitants of the academy appeared to be human with typical Starfleet knowledge. However during a conversation, one of the cadets, Valerie Archer, betrays her displeasure at breathing oxygen and sleeping. Chakotay then witnesses an alien beginning to revert from human form. Chakotay and Tuvok end their surveillance when confronted by one of the aliens who insisted they attend a meeting for unauthorized personnel. They render the alien unconscious and take him back to Voyager.
The captured alien committed suicide to prevent disclosing information when the Doctor attempted to extract DNA. Janeway and the crew are disturbed at the accuracy of the recreation and expressed concern that the facility is being used as a training ground for impersonating Starfleet personnel. The Doctor discovers that the guise is very difficult to detect (requiring microcellular scans to identify it as non-human).
The EMH managed to revert the corpse, which reveals its true form to be the lifeform known to the Voyager crew only by their Borg designation Species 8472. Several years before, in the "Scorpion" episodes, Voyager was attacked by Species 8472, but destroyed several of their vessels after forging a temporary alliance with the Borg against them. Voyager considers them the most dangerous and malevolent race ever encountered by humanity. Seven of Nine and the Doctor prepare enhanced nanoprobes and create warheads in case battle arises. Janeway still wants to opt for a diplomatic solution, but Seven presses the danger of the species and that it should be eradicated.
Janeway is convinced that the recreation is a precursor for invasion. Since they have no means to warn Starfleet, it is up to Voyager and her crew to prevent the invasion before it begins. Chakotay decides to follow up his date with Valerie to learn more. Harry Kim and Tom Paris wait in the Delta Flyer in case he needs assistance. Valerie reveals her mixed feelings about humans, remarking that they are genetically impure, but can create beautiful works. Chakotay says that perhaps humans are not as violent as they think. This raises suspicion in Valerie and she kisses him good-bye when they part. The obtained DNA sample reveals that Chakotay is human. She alerts the authorities, and Chakotay is captured while attempting to flee.
Tom and Harry alert Janeway that Chakotay is in trouble and they were unable to beam him out. Chakotay is interrogated by Boothby, and the aliens are convinced that Starfleet is sending ships to attack. Voyager arrives at the recreation facility and demands Chakotay be released. Tensions rise and weapons are pointed at each other, but no shots are fired. Janeway continues to press for a non-violent solution and invites the aliens aboard Voyager to discuss alternatives to war.
The talks start roughly. The aliens blame the Voyager crew for invading their fluidic space and destroying their ships. Chakotay tells Janeway that the aliens expect an invasion from Starfleet. Janeway does not manage to convince the aliens that Starfleet has not even heard about their species. The aliens reveal that there are multiple training grounds, and Voyager would be unlikely to find them all before an invasion. The aliens insist that they only defended themselves during previous encounters; Tuvok then asks, if this is true, why are they still in the Galaxy, obviously planning an invasion of Earth?
When the tension rises higher, Janeway lowers Voyager's weapons, saying: "One of us must put off his finger from the trigger, it might as well be me". This gains trust of Valerie and, against Bullock's direct order, she reveals that their planned infiltration of Starfleet Command is only a reconnaissance mission so that they are informed about an eventual planned aggression from Starfleet.
Bullock strongly warns against trusting humans, but Boothby, who is actually his 'superordinate', chooses to trust them. A truce is secured when Janeway agrees to provide information on their nanoprobe technology in exchange for the aliens' information on genetic alteration techniques. Boothby admits that it can be difficult to convince his superordinates, but he will try. Janeway and Boothby shared a discussion of peaceful co-existence, Chakotay and Valerie parted with a farewell kiss, and Voyager sees the last of Species 8472 for the remainder of their voyage home.