If the player joins the cult once again, they can help the cult destroy the city of Albuquerque, but they will die in the battle. In the Rebirth base the player can choose whether they join the cult once again or destroy the cult. The protagonist is, along with the Saviour, one of turned Ghouls so it means that they will die as well. The problem is that turning a Ghoul human again requires at least one normal person and the turned person later dies of tissue decomposition. The cult has a machine that turns ghouls into normal humans. Thomas reveals to the player that they are members of the Cult of the Rebirth, led by a person known as the Saviour. The player then finds a dying ghoul named Thomas, who claims they were the player's best friend. On their way they come across a group of ghouls who act as though they know the player and then proceed to try and to kill them. They start to search for hints of their past but the only clue they have is a mysterious talisman. The injured protagonist wakes up in a cave with amnesia. The story is set in 2170 in what was once New Mexico. Character creation is based on the SPECIAL role-playing system. Organized crime, prostitution and slavery are major elements of the setting. Mature themes such as alcohol consumption, drug usage and sex are present.

The player's actions dictate what future story or gameplay opportunities are available. General gameplay consists of traveling and interacting with local inhabitants and organizations to complete goals and aid or inhibit the NPCs. Combat and completion of jobs or quests reward the player with experience points with which they can level up their characters and apply beneficial perks to become more suited to the dangerous post-apocalyptic world. Injuries and poisons can reduce the number of action points available both in a single term and semi-permanently until combat ends and the player can be treated. If the player survives unharmed, they have their action points restored.

When a player uses up all of their action points, they end their turn and enemies start theirs. Combat gives them a number of action points to move, fire, check their equipment, reload and the like. The player is free to move at will until they enter into combat. The mod features the same gameplay as original games.

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