Naked Sin

Everything Begins

After destroying the Patriots' AI constructs, Meryl Silverburgh and Johnny Sasaki had their wedding at an undisclosed location. Roy Campbell finally returned to bury the hatchet with his daughter and give her away to her new husband. Also attending were Otacon, Sunny, Mei Ling, Jonathan, and Ed, who acted as the master of ceremonies and officially wed the couple. However, before the wedding could be completed, one final guest, Drebin, made an appearance providing the happy couple with a shower of flowers.

Drebin, drunk due to the nanomachines not metabolizing the alcohol for him any more, filled in the gaps for Otacon. He revealed that all of the Drebins were, in actuality, Patriot agents, which is why they were able to hack SOP so easily, and he was under orders from the Patriots to assist Snake and Rat Pt. 01 in their mission to exterminate Liquid. In fact, Rat Pt. 01 being an anagram for "PatR10t" (Patriot), finally left no doubt as to the team's true benefactors.

Sunny, meanwhile, had made her first outside friend, and asked Otacon if she could give him the Mk. III. Otacon obliged, and also told her that she could leave the Nomad if she wanted to. Sunny, however, only had one thing on her mind: Snake. After she asked where Snake was, Otacon became emotional, telling her that Snake was sick and needed some time to rest.

Meanwhile, at a hospital, Raiden was recovering from his operation, which had replaced his cyborg implants with ones more closely resembling a human body. As he rested, Rosemary entered with a mysterious young boy, but Raiden, at first, refused to speak to her. In tears, Rosemary revealed that both the marriage and her miscarriage were lies to protect them and Raiden from the Patriots, a cover for which Campbell had to sacrifice his own family. She also revealed that the boy she was with was Raiden's son, John. After one look at the boy, all the hostility and doubt in Raiden's mind was extinguished, and all three of them embraced, Rosemary promising to never let him go again.

Father & Son

Meanwhile, Solid Snake was, in actuality, visiting the grave of Big Boss once again. Collapsing in front of the grave, he vowed that the last thing for him to do - his final mission - was to take his own life, thereby erasing his genes and memes from the Earth, and removing the threat of the mutated FOXDIE strain. Finishing his last cigarette, he put his gun in his mouth and fired. In the end, however, Snake couldn't go through with it, and had fired into the air at the last second. The stress of nearly dying had apparently taken its toll, as Snake remained on his hands and knees, panting. In that moment, like a guardian angel, Snake heard someone say, "That's right. Good. No need for you to go just yet. It's been a long time Snake."

Snake turned to see Big Boss, very much alive, but also brandishing his mentor's gun. Believing that Big Boss had come to settle the score, Snake quickly reloaded his gun, but after a few minutes of holding each other at gunpoint, Big Boss dropped his gun, easily overpowered Snake, and embraced him, assuring his son that he was not there to fight. Telling Snake that it was "time to put aside the gun and live", he took Snake's gun from his hand, unloaded it, and threw it aside. He proceeded to explain that his body had been reassembled (using pieces of Liquid Snake and Solidus Snake) by EVA and Raiden rather than simply kept alive on a machine, and that the body in EVA's van that was burnt to ashes by Liquid Ocelot in Eastern Europe was in fact the body of Solidus. Ocelot was able to use the genetic code from this body to access the SOP system, because Solidus, unlike Liquid Snake or Solid Snake, was a perfect clone of Big Boss.

Big Boss then explained to Snake how Ocelot, in order to fool the system, used a mixture of nanomachines and psychotherapy to turn him into "Liquid's mental doppelganger", as well as fully explaining the history of the Patriots from his point of view. Once the virus opened the gateway from GW to the Patriots, Big Boss was able to finally determine the location of Zero. He then showed Snake an ancient, wheelchair-bound Zero on a life support machine, and claimed that the Patriots would not be completely destroyed until he "takes everything back to Zero" and "reduces Zero back to nothing". With that, Big Boss pulled the plug from Zero's air supply, euthanizing him.

With Zero dead, Big Boss was the last Patriot. When Snake asked if he would kill himself, Big Boss replied that he did not need to. The FOXDIE virus injected into Snake by Drebin that killed Ocelot and EVA was also set to kill Big Boss, and he was already starting to feel the effects. Big Boss explained that this FOXDIE virus also replaced the original mutated strain that Snake was injected with by Naomi, and therefore there was no threat of him becoming a biological weapon; though the new FOXDIE would eventually mutate as well, that would only be if Snake managed to live that long. Snake asked Big Boss if he was going to die, and Big Boss simply reminded him that all living things eventually die, and there was nothing that he could do to stop it. Snake helped his pained father over to The Boss's grave, where he saluted her as he had done fifty years ago and sadly stated that he had been dead since the day he killed her. Sharing one last smoke with his son, Big Boss, as a last request, asked Snake to spend the remainder of his life peacefully and not waste it fighting, and the two finally made peace. In his last words, Big Boss simply said, "This is good, isn't it?", and seconds later, the greatest soldier of the twentieth century passed away at the grave of the woman whose ideals had started it all and whose life and death had shaped him into the person that he was.

Sometime later, Otacon caught up with Snake and asked him where he was going. Snake, who had decided to quit smoking, responded that "there's one thing [he] still needs to do", that was to "see this age off [and] see what the future brings." Otacon insisted that he and Sunny accompany him to document the final days of his hero and friend and, after some persuasion, Snake agreed.

Later, Sunny was cooking eggs in the Nomad, finally making them perfectly. Proudly, she exclaimed:

"Sorta looks like the sun... it's rising again."

- Sunny