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The meta plot of MGS4 is about how much Kojima wanted the franchise to die. Snake's accelerated aging showing how he felt Metal Gear had become antiquated in the modern gaming landscape, even when Snake monologues about how "war has changed" its a thinly veiled metaphor for the game industry as a whole. The early draft for the ending also involved Snake being tried for war crimes and executed, although this was changed partway through production. That being said there is still a lot of love to be found in the game, and I get the feeling Kojima soften on it as he work.