On his way to rescue President Johnson, Raiden is confronted by the terrorist commander, who claims to be Solid Snake. Enraged by this, Pliskin reveals himself as the true Solid Snake and fires on the imposter from a helicopter. Utilizing an advanced exoskeleton, the terrorist leader evades Snake's attack and boards a Harrier being piloted by Vamp. Snake then tells Raiden to shoot it down, throwing a Stinger missile launcher down to him. After Raiden takes it down, the Harrier plummets, only to be caught by Metal Gear RAY. RAY proceeds to launch missiles into the air, destroying sections of the Big Shell and damaging the Kasatka, forcing it to land. RAY then departs into the ocean, taking the Harrier with it. After recovering from RAY's attack, Solid Snake contacts Raiden, introducing him to Otacon. They reveal they are there to stop the terrorists from using the new Metal Gear prototype. They also tell Raiden that Otacon has another reason for being in the Big Shell: to rescue his sister, Emma Emmerich. Raiden then proceeds to rendezvous and rescue President Johnson.

Once Raiden finally gets to the President, he is told about the Patriots, a mysterious organization that secretly rules over America. He also explains that the terrorist leader was his predecessor, the 43rd U.S. President George Sears, known by the codename Solidus Snake, a clone of the legendary soldier Big Boss, created in the "Les Enfants Terribles" project. Johnson adds that Solidus orchestrated the Shadow Moses Incident in 2005 but was removed from office by the Patriots. Solidus wanted to challenge the Patriots, unlike Johnson, who had simply wished to become one of them. Johnson also confirms that the Big Shell is merely a cover-up for the construction of Arsenal Gear, a gigantic mobile fortress that employs mass-produced unmanned Metal Gear RAYs to defend itself and can fire nuclear warheads from anywhere on the planet. It also has access to the Military's Tactical Network, granting it absolute control over the nation's armed forces and nuclear arsenal. However, Arsenal's true purpose is to filter information from the internet and other forms of digital communication using an AI called GW. By doing this, the Patriots hope to shape history as they see fit while maintaining the secret of their existence. Johnson’s last request is that Raiden locate GW's main programmer, Emma Emmerich, and provide her with a computer worm to eradicate the AI. Afterward, feeling he has said everything he needed to, Johnson suddenly grabs Raiden's gun, asking Raiden to kill him. Raiden resists, but Revolver Ocelot soon intervenes, shooting Johnson before Raiden can stop him.