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Synopsis

After learning that he has only a year to live due to Werner Syndrome-like symptoms, Snake is tasked by Campbell, now working with the United Nations Security Council, to assassinate Liquid Ocelot. In a war zone in the Middle East occupied by one of Liquid's PMCs, Snake meets Drebin, an arms dealer who injects Snake with nanomachines to use the latest weapons, and Meryl. Snake reaches Liquid, but the latter transmits a signal that neutralizes nearby people with nanomachines. Snake sees Dr. Naomi Hunter, who leaves with Liquid.

In South America, Snake locates Naomi, herself a captive of Liquid. She explains that Liquid plans to use Big Boss's biometrics to access and take control of the Patriots' gun control system. Snake learns that his accelerated aging is due to intentional genetic mutations as a human clone, and that the FOXDIE virus inside him will also mutate within a few months, spreading to the general population and causing a deadly pandemic. Liquid's PMC soldiers kidnap Naomi, but Snake saves her, assisted by Drebin and Raiden, and they escape, although Raiden is injured by Vamp.

Snake locates an Eastern European resistance group, which possesses Big Boss's comatose body, in order to cure Raiden. Her leader EVA reveals that she was Snake and Liquid's surrogate mother through the cloning process. They move Big Boss' body by boat while Liquid's PMC soldiers attack the decoys. Liquid captures the body and obtains the biometrics, aiming to infiltrate the Patriots' system using the repaired artificial intelligence (AI) core, GW, as a Trojan horse. American soldiers arrive to arrest Liquid, but he kills them after disabling their guns. Big Boss' body is cremated and Snake saves EVA from the fire when she attempts to save the body, but both are seriously injured in the process. Naomi leaves with Liquid, but Otacon follows them. EVA dies from her injuries.

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