Raiden awakens on Arsenal Gear, where Solidus reveals he had killed Raiden's parents and raised him as a child soldier during the Liberian Civil War. After this, Olga frees Raiden, explaining she is a Patriot double agent forced to help him in exchange for her child's safety. After the Colonel begins acting erratically, it is revealed that he is a construct of GW, damaged by the virus. Rose tells Raiden the Patriots had ordered her to become his lover and spy on him and that she is pregnant with his child. Raiden finds Snake, and together, they gain entry to Arsenal. Fortune then battles Snake, while Raiden is forced into combat with AI-controlled Metal Gear RAYs. The virus soon causes them to malfunction, and Olga sacrifices herself to save Raiden from Solidus.

Snake and Raiden are captured and taken to the top of Arsenal Gear by Solidus, Fortune, and Ocelot. Ocelot reveals himself as a Patriot agent and that the entire affair was orchestrated by the Patriots to artificially replicate a soldier (Raiden) on par with Solid Snake, titled the S3 Plan. Ocelot kills Fortune before being possessed again by Liquid Snake. Liquid explains that Ocelot's severed right arm was replaced with his own and plans to hunt down the Patriots using his host's knowledge and the stolen RAY. Snake pursues Liquid as Arsenal loses control.