In 2006, three years after the events of The House of the Dead 4, Kate Green joins forces with Ryan Taylor, the brother of her late partner and mentor, James, on an undercover mission in a dinner event within Scarecrow Manor, located in the outskirts of an unnamed U.S. state. The manager unleashes his army of mutant creatures upon the dinner guests. Realizing the threat to the world, Kate and Ryan then begin their quest to stop the manager and the outbreak he started.
As they progress through the mansion, they find clues related to the personnel of the DBR Corporation; Dr. Roy Curien, Caleb Goldman, and a mysterious man which Kate identifies as Thornheart, a descendant of the corporation's founding members, as well as the manager of Scarecrow Manor. Also during their exploration of the mansion, they fight gigantic mutants, such as resurrected creatures from the 1998 Curien Mansion incident, Chariot and Hangedman, as well as a new squid-like creature called the Priestess.
After escaping the crumbling mansion, Kate and Ryan fight their way through the zombies to a nearby church, where they meet Thornheart, who is revealed to be still alive. He reveals himself to be the mastermind of the game's events, and tells the agents that the corporation's purpose is to "cleanse" the world of its current status and "reshape" it in their own way. He then sets loose his masterpiece, The Moon, a tree-like behemoth which has abilities similar to that of the World from the fourth game. They fight it as it gradually became the shape of a humanoid and the size of a 20-story building. Ryan then tries to kill it in a desperate attempt by stabbing an iron rod through its head. This, at first, proves unsuccessful, but then a lightning bolt strikes the rod impaled through The Moon's head, thus electrocuting and killing it.
The next morning, Kate and Ryan rest as they watch the sun rise while the former recalls James's motto to never lose hope and keep fighting to the end.
There are four endings, depending on which location the player(s) choose one after the other. Unlike the previous games it does not include the zombified ending.
