In the Flesh

Voyager discovers a space station containing a near-perfect recreation of Starfleet Headquarters and Starfleet Academy, complete with staff and cadets. Chakotay goes undercover inside and discovers that the people there are Species 8472 in human form, training to infiltrate Earth. Chakotay makes a second trip and grows close to Commander Valerie Archer, who is also one of them. When his cover is blown, he is captured. The aliens reveal that they see the Federation as a threat, fearing an invasion after Voyager's alliance with the Borg, and they have been preparing to strike first. Rather than fight, Janeway invites their leader, who wears the face of Starfleet groundskeeper Boothby, to talk. Each side offers the other something in trust, including the nanoprobe technology Voyager used against his people. Chakotay is released, and both sides agree to step back from war.