One of Hideo Kojima's early ideas for the game's ending was to have Snake and Otacon turn themselves in to the United Nations for breaking the law (presumably for the crimes they committed while operating as Philantropy during Metal Gear Solid 2: Sons of Liberty), and be convicted and executed. The rest of the developers reacted negatively to this ending, which resulted in Kojima changing it. However, it's possible a remnant of this ending was left behind in the form of the game's end credits theme, a cover of "Here's to You", originally written for the 1971 Italian docudrama film "Sacco & Vanzetti". Both the song and film are based on the real-life case of two Italian anarchists who migrated to the United States in 1908, and in 1920 were convicted and sentenced to death after being accused of murdering two people during an armed robbery. The original 1971 recording of the song would later be used as the opening theme to Metal Gear Solid V: Ground Zeroes.

During the briefing for the second act of the game, Sunny can be seen walking around playing Penguin Adventure, the first game Hideo Kojima ever worked on, on a PlayStation Portable. If the player gets close enough with the Metal Gear Mk. II, music from the game can be heard playing.