Conducting a surveillance mission of an alien structure, Chakotay finds himself on Earth at Starfleet Headquarters. He is surrounded by aliens posing as humans, and strikes up a conversation with one of the women, Commander Valerie Archer. Later, when Chakotay and Tuvok are on their way back to the Delta Flyer, an alien Ensign tries to detain them for being in a restricted area. Unwilling to risk their cover being blown, they beam him back to Voyager.

When Janeway questions him, the Ensign kills himself by releasing a toxin into his bloodstream. The Doctor triggers a genetic reversion, and the body on the biobed turns into a Species 8472 alien. Analysis of their ship's structure shows the aliens are using a combination of holographic projection and particle synthesis to recreate Earth and Starfleet Headquarters. The crew surmises it is being used as a training ground for invasion of the Alpha Quadrant.

Seven of Nine discovers Species 8472 has adapted to Borg nanoprobes. As she works to modify them, Chakotay, Paris and Kim take the Delta Flyer back to the Earth simulation so Chakotay can keep a date planned with Archer. He plans to use her to find out more about the mission against the Federation. After Chakotay leaves her quarters, Archer analyzes a DNA sample and discovers that he is human. Once security is alerted, Chakotay is taken into custody.

Paris and Kim notify Janeway of what has happened and pilot their shuttle back to Voyager. The Captain sets a course for the alien ship, and is armed with modified nanoprobes but is unwilling to use them unless provoked. When she threatens the habitat leader — who is in the body of Starfleet groundskeeper Boothby — with the Borg nanoprobes, he agrees to a meeting.

With both sides gathered to discuss their differences, Janeway and Boothby find there is room for negotiation. Judging from Voyager's collaboration with the Borg against them, Species 8472 believed humans were a hostile force planning an invasion. Janeway explains that her crew did not know at the time that the Borg had started the war with their species; Archer then reveals that their Earth simulation is only a reconnaissance mission. They feared humans as much as the Voyager crew feared them. After agreeing to share technology as a first step toward peace between their species, the 8472 beings return to fluidic space, and Voyager continues on its journey home.