In 2002, somewhere in South America, Leon S. Kennedy and his partner Jack Krauser are searching for Javier Hidalgo, an ex-drug lord who had been reported to be approaching Umbrella, Inc. However, when Leon and Krauser reach the nearby village, they discover that the people there have been turned into zombies. Some zombies have the Sacred Snakes indentation, meaning that they worked alongside Javier. Leon and Krauser find their guide who, before he dies and has his body taken away by a water-bound BOW, says that the girl (Manuela) "brought devils to this village." Fighting their way past more BOWs, Leon and Krauser eventually find the girl, but have to face the creature that took their village guide. They successfully chase it off after Leon shoots the bell tower which causes it to fall on the creature. Krauser asks Leon to tell him everything about his encounters with BOWs. The scenario resumes after the Resident Evil 2 scenario.
Due to rising water levels, the survivors make their way to the water dam, where Javier and his BOWs await. Javier releases the monsters to attack Leon and Krauser while attempting to retrieve Manuela. It is revealed by Javier that Manuela is his daughter and that he had been tampering with the T-Veronica virus. The "Game of Oblivion" incident from Resident Evil - CODE: Veronica is shown. Leon and Krauser discover that Manuela has been receiving regular doses of the T-Veronica virus to contain her illness. At this point, Krauser finally pledges to Leon that he will view Leon as a worthy partner. Soon after, they learn that the reason Javier has been kidnapping young girls is because he was trying to extract organs to perform transplants in order to cure Manuela. Almost immediately, they are confronted by the gigantic monster that ambushed them back at the church, who they soon learn is actually Manuela's mother Hilda. Having the same illness as Manuela, she mutated due to the failure to keep the virus in check. Right before dying, she shoots out spikes from her body, one of which pierces into the arm of Krauser, wounding him. After defeating Manuela's mother, Javier merges himself with Veronica plant, becoming the V-Complex, then he attacks Leon and the injured Krauser; They manage to sever one of his arms, outside, Manuela assists Leon and Krauser in the battle against her father by using T-Veronica, at the risk of turning into a monster herself. The three survive, and are rescued by helicopter. The US government takes care of Manuela, and Leon and Krauser's story continues in Resident Evil 4. In Resident Evil 4, Leon discovers that Krauser now works for Wesker and they engage in battle, which ends with Leon critically wounding Krauser.
This scenario re-tells the events of Resident Evil 2, leading up to when Leon and Claire face G (a mutated William Birkin). Claire Redfield and Leon S. Kennedy have just arrived in Raccoon City, when they learn that the city has been infested with zombies and other monsters. They then decide to go to the police station, hoping to find answers. Claire and Leon are together much of the time, only briefly splitting up. When they meet Ada Wong, Ada fights alongside Leon, Claire and Sherry.
A re-imagining of Resident Evil CODE:Veronica, where Claire Redfield and Steve Burnside remain together and attempt to escape Rockfort Island in a seaplane, while having to contend with the psychotic Alfred Ashford, and eventually, his sister Alexia Ashford. In this iteration of the story, their father Alexander Ashford appears in a video, which was recorded shortly before he became the monster known as Nosferatu. Also, Alexia is portrayed as a much darker and sociopathic person, killing Alfred herself once she awakens and taking almost childlike pleasure in toying with Chris and Claire upon confronting them. Wesker and Chris also do not actually encounter each other, only getting a brief glimpse of each other in this iteration.
A hidden story of the game which tells the thoughts of Krauser during "Operation Javier". This scenario begins immediately after Krauser's acceptance of Leon in the middle of the game. As the trio goes deeper into Javier's hideout, Krauser's faith is shaken when he discovered the background of Leon. As he learns more about Javier's intentions with the virus, he finds himself beginning to accept Javier's way of thinking.
After his arm is injured during the fight against Manuela's mutated mother, Krauser's feelings of uselessness and embarrassment grow as he finds himself having to rely on Leon. He begins worrying about what will happen to him after completing the mission - with his wounded arm limiting his capabilities, he could easily be discharged from the military. During the final battle against the mutated Javier, Krauser sees Manuela using the power of the T-Veronica virus to fight her father. The demonstration of the T-Veronica virus further convinces Krauser that the dark side is the path he has to take, especially since he believes that the military will throw him aside once they learn of his injury.
After the mission is completed, Krauser discovers that there is no way to heal the damage done to his arm. Soon afterwards, Krauser begins searching for Albert Wesker, seeking the chance to repair his arm and gain more power.