The Hirogen programmed the prey to act and fight more realistically, eventually designing a subroutine to simulate the ability to feel pain. Combined with an ability to be regenerated after a simulated death, the holograms began to advance cognitively and became self-aware. The stress of pain created a much greater will to live among the holograms, and they eventually began to question their servitude and victimization.
On stardate 54315, a group of Starfleet holograms managed to win against the Hirogen hunters, killing 43 on the station. A distress call was received by the nearby Voyager, the ship which originated the holo-technology, and a responding away team discovered the various Hirogen corpses, murdered with Starfleet phaser rifles, Romulan disruptors and Klingon bat'leths.
One survivor, Donik, was found.
The holograms, led by Iden, rebelled against the Hirogen and escaped from the confines of the space station on which they resided. Following their successful rebellion, they destroyed a Hirogen ship and kidnapped The Doctor. As he spent time with the holograms, he became sympathetic to their plight and helped them thrwat an attempt by Voyager to deactivate them. During this incident, Iden kidnapped B'Elanna Torres to work on a photonic field generator with Kejal that would allow the hologram to colonize the Demon class planet Ha'Dara.
Using the stealth mode of their holoship, they managed to avoid Voyager long enough for the Hirogen to intercept Voyager. While the Hirogen threatened Voyager by telling them they would become prey if they attempted to track down the holograms, Donik showed the 5,000 meter-long ion wake produced by Hirogen vessels that would allow Voyager to follow the Hirogen to the holograms without being detected.
After the Hirogen detected the holograms, they hid inside a nebula and were pursued by the Hirogen. Iden eventually became unstable and megalomaniacal, wishing to establish a new holograph culture with himself as a god-like figure to be worshiped and prayed to. Iden viewed himself as a prophet on a mission to "liberate" holographs from their organic "oppressors". To this extent, he destroyed a Nuu'Bari mining vessel after it threatened to warn the Mining Consortium for taking its holograms. Even after learning that the holograms were non-sentient and could not support complex subroutines, Iden declared that they were "children of light and [he would] deliver them to freedom".
Shortly after entering orbit of Ha'Dara, the Hirogen entered the planet's vicinity and prepared to attack the holoship. before they could, Voyager disabled both Hirogen vessels. Iden sought to punish the Hirogen for hunting him and the holograms and subsequently transported them to surface the planet while taking the holoship into low orbit to avoid Voyager's attacks. Transporting a number of holograms to the surface, Iden deactivated the Doctor to use his mobile emitter in order to stage a massacre against the Hirogen.
Torres managed to convince Kejal to stop the massacre, but not before an attack on the holoship by the Delta Flyer disabled the holoship's transporters and communications. Due to the holoship's control over the generators, Kejal and Torres were able to deactivate the holograms loyal to Iden and send the Doctor down to the surface. Iden's program was then destroyed by the Doctor. (VOY: "Flesh and Blood")
The surviving Hirogen decided not to take the holoship, with the Alpha-Hirogen declared Voyager would have made worthy prey. Donik and Kejal took command of the holoship and left orbit for an unknown location. Prior to their departure, Captain Kathryn Janeway told them that while she couldn't tell them how to live their lives, she hoped they would consider the consequences of their actions. Janeway decided not to punish The Doctor, instead requesting a report on his "away mission". (VOY: "Flesh and Blood")