Scene deals heavily with cultural relativism, the idea that concepts such as right and wrong or allies and enemies are not absolute or eternal; but instead are personal and transitive, shaped by our cultures and the "times" we live in.
It is both the last canonical game and last Metal Gear game overall to be developed by KCEJ prior to the formation of Kojima Productions a year later.
This is notably the first canonical game to not feature a Metal Gear threat, as the Shagohod is actually an entirely different development project.
The major theme in Metal Gear Solid 3 is "Scene", the climate in which events occur and the impact it has upon them.
Although most Metal Gear games involve stopping a nuclear holocaust from occuring, this is the only game in the series to actually have a nuclear explosion occur early on in the game.
In order for America to clear its name and avoid World War III, The Boss' last apprentice, a man named John, also known as "Jack" and codenamed "Naked Snake", is dispatched by the special forces unit FOX to assassinate the woman who taught him everything.
Naked Snake is forced to kill his former mentor due to a "scene" he not only has no control over, but has no knowledge of.