Naked Sin

Meryl and Johnny
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, 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. Asking where Snake was, Otacon choked back tears, only able to explain to her that Snake was "sick" and needed some time to get better.

Raiden
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, Little 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.

Snake
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.

However, he could not do it, and had fired up into the air at the last moment. In that moment, like a guardian angel, appeared Big Boss, alive and unscathed. He explained that his body had been reassembled (using pieces of Liquid and Solidus) 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 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 or Solid, was a perfect clone of Big Boss.

Big Boss then explained to Snake how Ocelot, in order to full 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 to 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". With that, Big Boss pulled the plug from Zero's air supply, euthanizing him.

With Major 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 was also set to kill Big Boss. Big Boss explains that this FOXDIE virus would replace the original, mutated strain in Snake's system, and therefore there was no threat of him becoming a biological weapon. Before dying, Snake's father embraced his son in a fatherly hug, making Snake promise to cast off his role as a snake, and to spend his few remaining days as a man. Cigar in his mouth, hand raised in the salute he gave fifty years earlier, Big Boss passed away on the grave of The Boss, the woman that taught him everything.

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 to document the final days of his hero and friend and, after some persuasion, Snake agreed. Sunny, however, was not there to hear this; she was still cooking eggs in the Nomad, finally getting it right. Proudly, she exclaims:

"sorta look like the sun... it's rising again."

- Sunny