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Part I is called "When Man First Hit Man", which is not even a song really. According to Jay it's just an inside joke. It didn't become Part I until after Parts II and IV, which just seemed to fit the idea of tying How Could Hell Be Any Worse? with Suffer.
Neither Part II or Part IV came in as part anything; they were just called "The Numbers Game" and "The Index Fossil". However, they saw how The Numbers Game, Part III and The Index Fossil made a complete thought.
The song Part III is about world war three. Part II (The Numbers Game) is what precedes Part III, which is what precedes WW3, i.e. imperialism etc. And Part IV (The Index Fossil) is what comes after Part III and WW3, i.e. extinction.