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Buddy arrives, with JD revealing he was infected during the Ganados' attack after JD and Buddy share some words, Leon shoots and kills him. Leon returns to the church to find Ganados attacked it, finding JD as the only survivor. Ada leaves, warning the city will soon be bombed. Ada denies it and confesses retrieving a sample is her primary objective in the Eastern Slav Republic. Leon runs into Ada, who he thinks she's responsible due to her sample-retrieval mission during the Los Illuminados incident. JD helps Leon escape, urging him to stop Buddy a government bombing of a school killed Buddy's fiancee and her students, causing his hatred. Elsewhere, Leon meets JD, only for Plaga hosts to attack them Leon suspects the rebels possessed the Plaga parasites, which have escaped and infected them. Ivan tells Buddy to kill him, fearing his poor health is a burden Buddy reluctantly complies. Elsewhile, soldiers burst into the rebel hideout Leon tries warning them of Ivan's infection, but Buddy begins a shootout. and a human infected with the virus' dominant strain is possible. Ada explains a master-slave relationship between a B.O.W. Meanwhile, President Svetlana Belikova meets Ada Wong, who states herself as a BSAA agent. Leon awakens, tied to a chair by rebel fighters JD, Alexander Kozachenko (Buddy) and an eldery man named Ivan Judanovich (Ataman). A Licker attacks the pair and finishes off Scarecrow as Leon is knocked out by an explosion, a shadowy figure orders the Licker to not kill Leon which it mysteriously obeys immediately.
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Leon comes across his contact, "Scarecrow", who has been attacked and is near death. Determined to stop the biological warfare, Leon ignores the order. After his arrival, Ingrid Hannigan, Leon's mission support, informs him that the government has ordered an immediate retreat of all U.S. and Russia are preparing to intervene in. Kennedy sneaks into the Eastern Slav Republic to confirm rumors that biological weapons (also known as B.O.W.'s) are being used in the country's civil war, which the U.S.