Overview: A Hirogen hunting party has taken over Voyager and put its crew to work as living holodeck characters. Their minds are controlled by neural interfaces which make them believe they are their characters, and the Hirogen hunt them in two holodeck programs.
Captain Kathryn Janeway is a Klingon warrior complete with holographic cranial ridges when she is critically wounded by a Hirogen participating in a Klingon holodeck program. The Hirogen force the Doctor to treat her, with the threat that they would just let her die, and she is put back to work in a second, more spectacular program: the town of Saint Clare in Nazi-occupied France c. 1944. The Hirogen find Nazism fascinating, and are using the program to experience life in a military bent on conquering the planet. The Hirogen take on the roles of Nazi officers patrolling the town of St. Clare, with Voyager's brainwashed crew as their prey, members of the French Resistance.
Janeway is now Katrine, a French restaurateur and leader of the underground plotting against their Nazi occupiers. She works with a bartender (ship's tactical officer, Tuvok), who is loyal to the resistance movement, and a chanteuse and munitions expert (Seven of Nine). Voyager's Talaxian morale officer, Neelix, plays a baker who ferries messages and secret codes to the resistance headquarters. He is eventually wounded and transferred to the Klingon program after his recovery, and whose holodeck Klingon warriors would start taking down holodeck Nazis in street battles. Chief Engineer B'Elanna is a heavily pregnant French girl named Brigitte whose affair with a Nazi Captain allows her access to enemy areas.
The Hirogen enjoy using the Voyager crew in the simulation, because they are more rewarding to hunt down and kill than are holograms. In Sickbay, the Doctor is furious that he must repeatedly save his crewmates from life-threatening wounds sustained as they are hunted in the simulations. He is also distressed that there has already been one Voyager fatality. Ensign Harry Kim, who is being forced to expand the holodecks throughout the entire ship, works covertly with the Doctor to regain control of the ship and its crew from the Hirogen.
The Doctor finds a way to release first Seven, and then Janeway from their neural interfaces, and the two plan to break the Hirogen's hold on the rest of the crew. Just then, the Americans storm St. Clare with the help of the French Resistance. Captain Miller (First Officer Chakotay) and Lt. Bobby Davis (helmsman Lt. Tom Paris) arrive to take down the Nazi stronghold in the town, calling in an air strike to blow up German headquarters. The explosion overloads the holo-projectors' already strained circuitry and blasts an opening from the holodeck into the rest of the ship. Holograms invade Voyager and the ship's interior becomes a World War II battleground.
Janeway fights off holo-soldiers and Hirogen Nazis to plant explosives in Sickbay. When it blows, the neural interfaces release the Voyager crew and they find themselves immersed in a war, or in the case of Neelix and The Doctor, amidst a group of drunken Klingons. Meanwhile, the leader of the Hirogen captures Janeway and she realizes what he is trying to do. His own culture will never survive with their lifestyle of wandering in scattered hunting parties, and if he could establish holo-programs his people could stay together and experience countless hunts of all kinds. Janeway takes advantage of his wisdom and the two establish a truce.
Unfortunately, one of the other Hirogen has become inspired by Nazi philosophy. He assassinates his leader and aims to conquer Voyager's crew in the spirit of righteous domination. Just in time, Neelix and the Doctor manage to merge the holo-programs, unleashing the murderous Klingons on the Nazis just seconds before they can execute the Voyager crew. Harry overloads the holodecks and the program finally ends.
After days of fighting, a truce is called between Voyager's crew and the Hirogen. The Hirogen agree to leave Voyager in exchange for holodeck technology.