The Doctor, who voluntarily joined the renegades, is furious with the group's leader, Iden, but Iden promises to let Torres go once she has a chance to decide for herself whether to help the Holograms. Meanwhile, the Voyager crew struggles to repair the ship in Torres' absence, and Janeway learns that the Doctor betrayed and abandoned the ship, and wonders if his matrix may have been altered by the other Holograms. When Torres wakes up on the Hologram ship, she intends to leave immediately, and rebukes the Doctor for switching allegiances. The Doctor points out she did the same thing as a Maquis, and tries to convince her that by providing her technical expertise, she can help stop the violence. He takes her to meet Iden, and she agrees to look at the photonic field generator, but makes no promises.
On Voyager, the crew has no luck locating the Holograms. Donik thinks he can modify the ship's sensors to detect them, and asks to stay aboard rather than go back with the other Hirogen. Two much larger Hirogen vessels arrive and retrieve all their people except for Donik, and the new Alpha-Hirogen threatens to turn the Voyager crew into prey if they interfere with their hunt. The Hirogen vessels go to warp, and Janeway decides to follow using a plan by Donik to hide Voyager in the ion wake of one of the Hirogen vessels — a "blind spot."
Torres looks at the photonic field generator with Kejal, suspicious of the Holograms' motivations. When she comes to realize she's prejudged these beings, Torres proceeds to help enhance their technology. Meanwhile, Iden approaches the Doctor, who is having doubts about being with the Holograms. Iden shows him their destination: a Class-Y planet he calls "Ha'Dara," which is Bajoran for "Home of Light." He plans to install the generators on that planet because its environment is toxic to organic life, so they'll be left alone there. Just then, the Holograms realize that two Hirogen vessels have detected them, so they proceed to hide in a nebula. The Hirogen ships also fly into the nebula, unaware that Voyager is trailing one of them from within its ion wake.
The Holograms try to evade the Hirogen while Torres works a little faster to get the field generator on line. She successfully tests the generator by running Kejal through it, and lets the hologram know that as the closest thing they have to an engineer, she's the most important member of her crew. Meanwhile, the Doctor tells Iden that in their new society on Ha'Dara, he hopes to expose the others to music and art from various worlds. Iden responds that the Holograms will develop a culture of their own without emulating organics. In fact, he plans to establish a new religion with himself being worshipped as the "Man of Light" who delivered his people to freedom. The Doctor's doubts grow stronger.
A Nuu'bari mining ship is detected, and Iden orders an intercept course, planning to liberate the holograms on board. The Doctor expresses his concerns to Torres, revealing that Iden is showing signs of megalomania. Meanwhile, the Hirogen detect the Hologram ship on the other side of the nebula and move to intercept, with Voyager surreptitiously tagging along. On the Hologram ship, Iden contacts the Nuu'bari miners and tries to coerce them to turn over their holograms. They refuse, so Iden fires upon them and has Kejal steal the hologram programs. The Nuu'bari threaten to retaliate, so Iden targets torpedoes upon their warp core and destroys them, to the Doctor's and Torres' horror. He then sets a course for Ha'Dara as Torres accuses him of murder. He has her confined and then asks Kejal to bring their new "friends" on-line. Because their programs are incompatible with their emitters, she needs Torres' help, who agrees because she thinks she can get through to Kejal. As they work, Torres lets Kejal know that Iden doesn't have to be the one to make all the decisions, and she has the power to deactivate him. Finally the Nuu'bari holograms come on-line, but they are incapable of any interactions — they are only programmed with very rudimentary subroutines. Torres points out that Iden killed two living beings to "liberate" mindless machines, but Iden fervently declares that they are "children of light" and he will deliver them to freedom. Just then the bridge announces they are approaching Ha'Dara. Iden orders the generator to be deployed immediately, and refuses the Doctor's request to release Torres.
The Hirogen follow the Holograms to the planet, and when they drop out of warp, Voyager immediately fires weapons and disables both hunting vessels. Voyager then turns on the Hologram ship. Iden has the Hirogen hunters transported to the planet's surface so that the Holograms can hunt them in retaliation. The Doctor objects to his actions, so Iden deactivates his program, but not before assuring him that he'll be remembered in their prayers. He takes the Doctor's mobile emitter and transfers his own program to it, and orders the field generator transported to the surface. He rallies the other Holograms, declaring that this time, the hunt is theirs.
On the surface, the unarmed Hirogen have trouble breathing. The Holograms materialize around them and begin pursuing them with weapons. Meanwhile on the ship, Torres convinces Kejal to stop the massacre, but their transporters and communication system were damaged by Voyager. Torres tells Kejal to shut down the Holograms, which she does, and the Holograms on the surface dematerialize before they can kill more Hirogen. However, Iden is using the mobile emitter, so she can't deactivate him. Torres suggests sending the Doctor to the surface through the generator.
The Doctor materializes on the planet with a Hirogen hunting rifle, and he begins pursuit. Just as Iden is about to kill the Beta-Hirogen, the Doctor catches up with him and demands he lower his weapon. Iden refuses, so the Doctor fires and obliterates his fellow Hologram.
The surviving Hirogen are rescued by Voyager, and after recovering, the Beta-Hirogen intends to reclaim the Hologram vessel along with everything in its database. But Neelix convinces him that the stories that are told about this hunt will reflect more favorably upon him if the Hologram ship is thought to have been destroyed. The Hirogen agrees, and leaves Voyager empty-handed. Janeway transports to the Hologram vessel and learns from Torres that Iden is unrecoverable, but the other Holograms are intact in the database. Janeway offers Kejal refuge on Voyager, but she insists that this ship is her home, and Donik volunteers to stay with her and reprogram the Holograms to undo some of the damage he caused. Torres vouches for them, and Janeway urges them to always consider the consequences of their actions, which she's saying just as much to herself as the others. Back on board Voyager, the Doctor offers to let Janeway take his mobile emitter away and revoke his freedom, but she won't punish him for becoming as fallible as those who are made of flesh and blood.