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When the EDF air transport takes you to your monster truck in the desert, you're told that you cannot reach the dam directly because a Battlelord there is shooting down every approaching aircraft. So why can an air transport reach the dam and pick up the president? Because he is in cahoots with the aliens!
The behavior of the NPCs in the Titty City level is extremely unrealistic: they talk to Duke, or about Duke, as if their whole lives revolved around him; they repeat the same phrases, over and over, every time Duke approaches them; in one of the toilet stalls there's Bombshell, giving oral sex through a glory hole (this can be verified by cheating and comparing the face of the girl in the toilet with Bombshell's face on page 361 of the Balls Of Steel Limited Edition Guide). This is not a case of They Just Didn't Care: their behavior does not match what we would expect in reality because the whole level is a dream!
For the first few minutes of the DLC, Dr. Proton is speaking to Duke via audio only. Duke fails to recognize Proton at first because this is the first time he or the player got to hear Dr. Proton's voice; the last time the two saw each other, there was no voice acting for either of them.