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What Could Have Been: The original plan for the first game called for the plot to branch at various points depending on how many BoBs you saved in certain levels. This was scrapped and the only remnant of that plan is differing messages from Leela depending on how many of them you saved.
It is worth noting that the capacity to do this was still built into the engine, and that when a player transitions from the end of one level they can (in theory) be sent to any other map-maker defined level in the game, regardless of level order. While conventionally the player is sent to the next level in the order, some mod-makers have taken full advantage of this ability to alter the next level that the player goes to based on what they accomplished in that level, with resulting branching plotlines.