Battle in Arsenal Gear

The Set-Up and Battle
After Otacon had left to rescue the hostages, Snake mentioned to Raiden that they may need a hand getting inside. Just then, the Cyborg Ninja appeared once again and revealed himself to actually have been Olga in disguise. Raiden was then knocked unconscious by Olga, with Snake saying that he didn't ever recall saying he was on Raiden’s side.When Raiden came to, he was tied to a torture bed completely naked. Solidus and Ocelot talked to him, with Solidus remembering that he taught Raiden everything he knew during the Liberian Civil War, when Raiden's real parents died. He was the star of Solidus' Small Boy Unit, earning him nicknames like "Jack the Ripper" and "White Devil." Solidus now had an eye patch over his left eye (which was damaged when Raiden took down the Harrier) with Ocelot commenting that he was the "spitting image of Big Boss." After Ocelot left, Olga walked in and told Raiden about her child, whom she had never met because she was stolen by the Patriots. Olga told Raiden that if he were to fail this mission, her child would be killed. Olga could not let this happen, and she had been sent in by the Patriots to assist Raiden. She told him that Snake was waiting up ahead, before leaving the room. Raiden then received a call from Rose, asking him if what Solidus said was true, which he admitted. He had been a child soldier, raised by Solidus to be a ruthless killing machine. After making his way through the hangar which housed many mass-produced Metal Gear RAY units, he was called by Rose again who nervously told Raiden that she had been a spy for the Patriots all along. She became his girlfriend, simply to keep an eye on him, but truly fell in love with him. She changed her appearance to suit his desires, but her transmission was eventually cut-off with her final words being "Jack… I’m… pregnant, Jack…your baby" Fortune blamed Solid Snake for her father's death. After his bonds were released by Olga, a distressed Raiden pressed on and met up with Snake. Snake apologized for his earlier "betrayal" saying he needed to use Raiden to sneak his way into Arsenal Gear. The two then battled their way through the Arsenal Tengu and, on the way, Otacon discovered that the Colonel Campbell who had been helping Raiden throughout the mission, wasn't the real Colonel, but an AI created by GW, cobbled together from Raiden's hopes and expectations. Just then, Snake was confronted by Fortune, who had been waiting for Snake as she believed that he killed her father, Scott Dolph. Snake and Fortune prepared to battle as Raiden headed up a nearby ladder, and Raiden appeared on a giant platform. Concealing his presence, Solidus called out to Raiden, telling him of the S3 Plan, or Solid Snake Simulation, which had been devised to create the perfect warrior through VR training; training which Raiden had previously undertook. Raiden was then forced to battle a horde of Metal Gear RAYs, destroying several with his Stinger missile launcher, before eventually giving in to exhaustion and falling to his knees. As Solidus emerged from his hiding place, he was ready to kill off Raiden before Olga jumped out in front of them, confronting Solidus. As she gave her life to save Raiden and, therefore, her child, Solidus ordered the remaining RAYs to kill Raiden, but Emma's GW virus started to take effect. Angered by this new development, Solidus destroyed the remaining RAYs and cursed the Patriots. As Fortune entered the area with a handcuffed Snake, Raiden passed out.

Aftermath
Ocelot successfully escapes with Snake in pursuit and Raiden defeats Solidus. As Raiden stood outside the front of Federal Hall, Snake appeared and informed him that he and Otacon were going to find the Patriots using the virus disc (since it had been programmed to censor the names of the Patriots' leaders, it would have some form of indicator to identify what those names were). Raiden insisted on coming with them but Snake told him to stay, telling him that he still had things to do and "people to catch up with." Although the mission had been a simulation, Snake comforted Raiden with the fact that everything he had felt during the mission was his and his alone: it was up to him to decide what to pass onto the future, and to figure out his own purpose for himself. After Snake departed, Raiden was reunited with Rose, and the two vowed to make a life together, both figuratively and literally.

Sometime later, Otacon and Snake "successfully" traced the Patriots, but discovered that all twelve of them were dead, and had been for the last hundred years. Snake deduced that the information retrieved from Arsenal Gear was false; it was only a fake lead orchestrated by the Patriots. With this, Philanthropy Unit had lost their only lead, the future of the Patriots uncertain.