The Federation starship Voyager discovers an injured Hirogen who is in the middle of an intense hunt for what is a formidable and dangerous prey even for Hirogen standards. He is brought in to Sickbay for treatment, but is eager to get back out and track down his trophy prey. Before he is able to do so, the prey alien invades Voyager. It is a tough, armored, telepathic, insectlike creature that the Borg have designated Species 8472.
The Hirogen hunter is allowed to hunt for 8472 under Chakotay's supervision. The Hirogen starts attacking an unresponsive 8472 without hesitation. He refuses an order to stand down and battles with his Starfleet escort before being stunned and subdued; he is subsequently confined in sickbay. As the crew later approach the seriously injured 8472, it telepathically communicates with the Vulcan tactical officer Tuvok, pleading to be rescued from the hunter and returned to its home, which is a different dimension known as "fluidic space." Meanwhile, a number of Hirogen vessels surround Voyager threatening to destroy them unless 8472 is beamed over. Nevertheless, Captain Janeway immediately orders Seven of Nine to help the alien return to its home territory, hoping to open the door to peaceful contact with its species. Seven refuses to comply, believing the protection of the hated and feared alien is not worth facing imminent destruction at the hands of the Hirogen. She informs Janeway that the approaching Hirogen ships will destroy Voyager unless 8472 is turned over, and a lesson in compassion will do her no good if she is dead.
As Hirogen ships open fire on Voyager, shield generators are temporarily disabled allowing the Hirogen hunter to escape from Sickbay. The hunter corners 8472 and grapples with it at which time Seven beams both of them to one of the Hirogen ships nearby. By giving 8472 to the Hirogen, Seven has blatantly disobeyed Janeway and assured the creature's death although she tries to justify her actions as being necessary to save the ship. Janeway disciplines her with limits on her computer access privileges and restriction to the Cargo Bay.