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In 2004, a 27-year-old Leon was assigned to a top-secret organization under the direct control of the President of the United States. He is assigned to guard President Graham's family, but when the President's daughter, Ashley Graham, is kidnapped, Leon's first mission is to track her down. Information gathered pointed to the kidnappers being located in a remote area of Spain. Leon investigates on his own, along with two members of the local police. Unfortunately, it seems something bizarre has happened to the local townsfolk and after the two officers are promptly killed, Leon finds himself relying on his skills once again in a deadly fight for survival. Leon learns from his superiors that the perpetrators are a group called "Los Iluminados" (from Spanish, meaning "The Illuminated" wink , a religious cult led by a man named Osmund Saddler. This cult uses a mysterious parasitic organism known as "Plaga" (Spanish for "Plague" wink to take control of the local townsfolk, as well as many others around the area, such as a group of Mercenaries. Although a seemingly hopeless situation, the fanatical cult finds the formidable Leon to be more than they bargained for as he foils attempt after attempt to kill him. During the course of his mission, Leon is helped by Luis Sera, a man who is revealed to be a researcher who used to work for Saddler, but betrayed him. Leon also once again has a chance encounter with Ada, who is also involved in this incident. She provides assistance to Leon, but has a fight of her own to battle out, as well. Leon is assisted by Hunnigan, an information analyst and fellow government official via a communicator. As Leon progresses, however, he finds the transmission hijacked by the cult and he is forced to fend for himself.

Leon eventually finds Ashley in a church and he becomes responsible for her safety as the two make their way around the Los Illuminados-controlled area. It is revealed, however, that both Leon and Ashley have been injected with the Plagas and are now in a race against time to find a cure for this before they are forever turned into Saddler's slaves. Acquiring weapons from a mysterious merchant with a Cockney accent, Leon manages to fight his way through many harrowing perils within the local village and a mysterious Castle run by the cult. He eventually fights against two of Saddler's underlings, village chief Bitores Mendez and the Castle's castellan, Ramon Salazar. Leon also confronts his former comrade, Jack Krauser, who was now working as a double agent for both a mystery party and Saddler. It is revealed to the player (but not Leon, necessarily) that this mysterious third player in the conflict is none other than Albert Wesker, whom Ada is also working for. Unknown to Leon, a secret battle is being waged behind the scenes, which is explored in Ada's unlockable scenerio, "Separate Ways". Eventually, Ashley is abducted and Leon must race against time to rescue her before her Plaga fully develops, not to mention his own. With continued support from Ada, Leon fights his way through a local military base, where Saddler and the cult have taken refuge. Fighting against both a deadly enemy and the enemy within, this battle tests all of Leon's strength and skill. Leon fights against Krauser for the last time and eventually saves Ashley and himself after removing Las Plagas from within them by use of a special radiation machine developed by Luis late during his mission. Afterwards, Leon battles Saddler in his true form and, with Ada's help (who provides him with a specialized rocket launcher), is able to put an end to him and his plot.

After the battle, Ada takes the Plagas sample from Leon and makes her getaway, but gives Leon and Ashley a means to escape, as well, via a jet-ski. Ashley invites Leon to her residence for "overtime", but Leon politely declines. Despite this turn of events, Leon is aware that he still may have not shed his affection for Ada, the "part of him he can't let go." After completing his mission, he talks with Hunnigan, who finally manages to re-establish contact. He compliments her on her appearance (she isn't wearing any glasses at this point) and lightly flirts with her by asking for her number, to which she reminds him that he's "still on duty". Upon being left in the dust by a second woman, Leon can only reply with an amused sigh, "...story of my life."