Two Hirogen move through a jungle hunting prey. Suddenly phaser shots are fired at them from a small lake. Four armed Starfleet crewmen rise out of the water and continue firing, destroying their predators with vengeance.
The U.S.S. Voyager receives a distress call on a Hirogen frequency and approaches a mysterious vessel. An away team beams over and finds themselves in a jungle, and upon surveying the area, they discover the bodies of Hirogen killed with Starfleet-issue phasers. They are also surprised to find a Klingon bat'leth stained with Hirogen blood. The team detects a lifesign that appears wounded, and upon approaching a cave, they are fired upon. A panicky Hirogen civilian, Donik, warns the visitors away and continues firing his weapon. Tuvok sneaks up behind Donik and renders him unconscious with a nerve pinch. The Hirogen has lost a lot of blood, so Paris beams him to Voyager's Sickbay. Meanwhile the away team finds a holodeck interface of Starfleet design, and they realize the jungle environment is simulated, and wonder why their tricorders didn't detect that fact. Seven of Nine shuts down the holodeck emitters, and they find themselves in a hologrid filled with dead Hirogen.
Back on Voyager, Chakotay tells Captain Janeway the holo-technology she gave the Hirogen three years ago so they could hunt holographic prey was apparently modified to be more dangerous. The Captain is astonished that the Hirogen obviously "missed the point" and got themselves killed. She approaches the terrified Donik in Sickbay, and after convincing him she is not a Hologram, learns that the vessel he was on is a training facility where young Hirogen learn to hunt. He is a technician who was maintaining the system when the Holograms malfunctioned, took control and deactivated the safety protocols.
Just then, a Hirogen ship intercepts Voyager and starts firing. The Alpha-Hirogen in command demands that Voyager leave immediately, but Janeway informs him that she has the one survivor from the facility on board. The Alpha- and Beta-Hirogen beam over and confront Donik, accusing him of being a coward for hiding from the Holograms while hunters fought and died. Donik reveals that the Holograms transferred their programs to a vessel equipped with holo-emitters, and are on the loose.
The Hirogen team up with Voyager's crew to locate the renegade Holograms. Once they detect their ship, the Hirogen prepare for the "hunt" and Janeway insists on joining them, feeling partly to blame for the situation. The Hirogen vessel moves in for the kill over Janeway's objections, and after it's too late they realize the ship they see is a decoy — it's really a bomb, which explodes and seriously damages the Hirogen vessel. While Voyager beams over the survivors, the actual ship occupied by the Holograms drops out of warp and starts firing. The Holograms then tap into the holo-emitters in Sickbay and transfer the Doctor's program to their own ship, then immediately go to warp, masking their signature so they can't be followed.
The Doctor materializes on the Holograms' ship and finds himself surrounded by simulations of various Alpha Quadrant species. A Bajoran hologram named Iden welcomes the Doctor aboard. He demands to be returned to Voyager, but Iden says they have "wounded." The Doctor says he's not an engineer and has limited experience in repairing holograms, but Iden insists that he try.
At Voyager, Janeway learns that the Holograms are very sophisticated and have the ability to learn and adapt, so they will be hard to disable. Donik confesses that he modified the Holograms under his Alpha's orders to make them formidable prey. Janeway approaches the Beta-Hirogen, who is in charge now, and lets him know she found out about the modifications, and points out that they created prey with skills that surpass their own. The Beta-Hirogen says he will resume the hunt, but Janeway insists they must find a way to take the Holograms offline from a safe distance, and do it with the Hirogen's help or else she'll leave them on the nearest habitable planet. The Beta-Hirogen has no choice but to agree.
At the Hologram ship, the Doctor finds a way to perform a "subroutine transplant" in order to repair a Klingon hologram, and succeeds with the help of Kejal, a highly intelligent Cardassian hologram. The Doctor is shocked to find Holograms bleeding and experiencing pain, and Kejal explains that the Hirogen programmed them to suffer when they are killed. Once he's done treating the injured, the Doctor finds Iden praying at a Bajoran altar, and wonders how someone who's programmed with spiritual beliefs could perform such a massacre. Iden explains that his Alpha-Hirogen would hunt him and kill him over and over, causing him to live in fear and pain. With the ability to adapt, he became cunning enough to escape, and joined other photonic beings who were being oppressed by various races in the sector and who had chosen to fight back. The training facility they just left was actually the third one where Iden "liberated" the holograms. Iden tells the Doctor his life will never be his own as long as he is controlled by organics, and asks him to stay and make a new life with his own kind. The Doctor refuses.
Soon after, the Doctor finds himself running through a jungle, being hunted by Hirogen. The confused and terrified Doctor gets wounded and starts bleeding, then he's stabbed to death. The Doctor wakes up in shock on the Hologram ship. Iden explains that they transferred memory files from one of their Holograms into his program so he can come to understand what they've been through. Enraged, the Doctor accuses them of being thugs looking for a fight. But Iden says what they're looking for is a home where the Hirogen can't hurt them anymore. His sympathy growing, the Doctor asks to hear more about this "home." Iden and Kejal show the Doctor a photonic field generator, which they plan to deploy on a planet's surface to create a holographic environment they can live in. The Doctor suggests that the Voyager crew could help, especially Lt. Torres, who's an expert on holo-emitters. Iden does not trust organics, but is interested in knowing more about Torres.
At Voyager, Donik discusses strategy with Janeway, Seven of Nine and Torres on how to shut down the Holograms, and Torres embarks on a plan to reconfigure the ship's deflector to emit an anti-photon pulse. Soon afterward, the Hologram ship intercepts Voyager and hails them. The Doctor appears on the viewscreen and says the Holograms have come to make peace. He comes back aboard and tells Janeway that the Holograms want to create a new life for themselves and need Voyager's assistance. Janeway is hesitant to share technology again, because that's how the problem got started. The Doctor gets frustrated and tells her the Holograms are a new species, one that she helped create, and she can't turn her back on them. Janeway and the Doctor argue contentiously over "holographic rights" when they get word that a fight has broken out in the Mess Hall where the Hirogen are being confined.
The Hirogen are creating chaos so that the Beta-Hirogen can get to a control panel and access the com system. Tuvok arrives and stops him, but he has already summoned two Hirogen vessels. With less than an hour to intercept, Janeway orders Torres and Donik to prepare the deflector to take the Holograms off-line so there will be no more bloodshed. The Doctor objects to having them deactivated, but Janeway proceeds and contacts Iden, telling him to prepare his people to be transferred to Voyager's database. Iden doesn't trust that Janeway, an organic, will ever reactivate them. He ends the transmission, fires on Voyager and begins moving away. The Doctor pleads for Janeway's reconsideration, but she orders him to go help Paris treat the wounded in the Mess Hall. The Doctor leaves the Bridge, but in a crisis of conscience, goes to Sickbay instead. He contacts Iden and transmits data on the pulse about to be used to deactivate the Holograms, along with Voyager's shield frequencies so they can beam him off the ship. The Doctor transports over while Voyager and the Hologram ship exchange fire. Iden had given his word he wouldn't use the shield frequencies to attack Voyager, and he keeps that promise, but when Voyager emits the deflector pulse, he sends a feedback surge through the beam that overloads the ship's deflector and causes an imminent warp core breach. As Torres puts up a forcefield to reinforce the core, an energy tendril knocks her out. Iden beams Torres over to his ship, then escapes to warp as Voyager is left adrift.