Meryl and Johnny are married. Their wedding, held on an airfield, is attended by the members of Rat Patrol, Otacon, Sunny, Drebin, and Campbell. Meryl reconciles with Campbell. Raiden's cybernetic body is reverted to an organic form through surgery, and he reunites with his fiancée Rose and their son. Rose reveals that her marriage to Roy Campbell was a charade to keep her protected from the Patriots during the course of Raiden's mission. Snake attempts to commit suicide in the graveyard housing the graves of Big Boss and The Boss in order to prevent his mutated FoxDie strain from spreading further, stating that killing himself is his "final mission." Drebin reveals to Otacon that the Patriots forced him to work as a gun launderer, and that Rat Patrol 01 was also manipulated by the Patriots.
After voice actor credits, it is revealed that Snake couldn't kill himself, and he is congratulated for not doing so by a distinct voice, who turns out to be a resurrected Big Boss. Big Boss tells Snake that the body burned on the Vltava was actually Solidus, and that he was reconstructed with surgery using parts from both Solidus and Liquid's bodies. He brings Major Zero along with him, now extremely elderly and confined to a wheelchair in a vegetative state. Big Boss explains Zero's motives for creating the Patriots, and subsequently euthanizes him. He reveals that Ocelot and EVA had left the Patriots, and had since had been working to destroy them. He also reveals that Ocelot used hypnosis and self-suggestion, as well as nanomachines, to mentally transform himself into Liquid's dopplegänger in order to fool the Patriots. Both Ocelot and EVA were killed by a new strain of FoxDie injected into Snake (by Drebin, in Act 1) that also neutralized the older FoxDie strain. After telling Snake this, Big Boss also reveals that the newer FoxDie is already affecting him. He finally makes peace with Snake and before dying on The Boss' gravestone and saying: "This is good... Isn't it?".
In the coda, Snake explains to Otacon that he will spend his remaining days attempting to simply live his life (and also plans to quit smoking). Otacon wishes to come with him in order to chronicle the last days of Solid Snake. Snake initially refuses but with some persuasion ultimately relents, allowing Otacon and Sunny to accompany him.
