Following the harrowing escape from Raccoon City, Leon S. Kennedy, Claire Redfield, and Sherry Birkin initially lived together. Claire took on a strong, almost maternal role in raising Sherry, with Leon's support. Even during this time, Leon was haunted by the memory of Ada Wong, the enigmatic spy. Though her loyalties were questionable and she pursued nefarious goals, she ultimately saved his life. Despite learning of her apparent death, Leon continued to dwell on her actions. On the morning of September 30, the group was forced to split. Claire continued her search for her missing brother, Chris, while a wounded Leon took care of a weakened Sherry. Seeking protection, they approached the U.S. military stationed outside the city, where they were immediately apprehended. Sherry was placed into protective custody as a research subject, and Leon was taken in for an intensive interrogation by Adam Benford, a high-ranking government official and military intelligence officer. Leon was deemed to know too much about the Raccoon City incident. However, his survival demonstrated anti-B.O.W. skills that were in high demand, especially given the military's failure to secure the G-Virus. He was presented with an ultimatum: in exchange for his own life and Sherry's safety, he was recruited into a classified anti-Umbrella military agency formed rapidly after the disaster to prevent future outbreaks, reporting directly to the President. He was trained by an elite operative named Jack Krauser, and the two men quickly formed a close bond. Their first major mission together was a joint operation in South America where they saved Manuela Hidalgo and defeated her father, Javier Hidalgo. They confronted Javier after he had monstrously fused with a plant infected by the t-Veronica Virus. Manuela helped them by unleashing the virus's effects on her father, leading to Javier's death. Manuela was taken into government custody. Leon and Krauser parted ways shortly after, as Krauser was discharged due to a severe injury sustained during the mission. Later that year, Leon was informed that Krauser had been killed in a supposed accident. In 2004, President Graham’s daughter, Ashley Graham, was abducted while returning home from the University of Massachusetts. The details of the operation suggested the hallmarks of an inside job. American intelligence tracked her to a remote village in Spain. With government agencies under intense scrutiny due to a suspected mole, Agent Leon S. Kennedy was deployed alone to investigate. He arrived with two municipal police officers from Madrid, maintaining a low profile for the classified rescue operation.

The rain was a whisper, a soft, persistent shushing against the glass that did little to disturb the oppressive quiet inside the car. Rain had a way of dredging up the past. It was raining the night Raccoon City died. Rain pattered lightly against the windshield as the police car wound its way through the fog-choked roads of rural Spain. The forest loomed on either side, gnarled and lifeless, the kind of place sunlight seemed to avoid. Inside the vehicle, Leon S. Kennedy sat in the back seat, his sharp blue eyes fixed on the blurred reflection of the trees sliding past. His gloved fingers idly adjusted the earpiece in his ear before he thumbed his radio. “This is Agent Kennedy,” he said, his voice steady but edged with weariness.

“I’m approaching the drop zone. Still no visual on the village.”

The static hiss that followed was a familiar companion. Six years of static, of clipped orders and mission reports that barely scratched the surface of the horrors they described. Six years since his life had become someone else’s property. He let his hand fall to his lap, the worn leather of his jacket creaking with the motion. The gloom outside the car was a mirror to the haze of memory. For a few short weeks after the escape, there had been a flicker of something resembling normalcy.