Non Standard Game Over: at the very beginning of NORAD VI in the Turbo edition. Go here and skip to 5:40. The only thing discernible is that the canister of sleeping gas was meant to be removable and become a death hazard, but was improperly programmed and it wasn't until Pegasus Prime that the proper scenario came out.
What Could Have Been: In the original Journeyman, one of the memory chips has a recording of the Big Bad talking about how he aims to blow up Caldoria with a nuclear bomb should his plans fail. This doesn't happen since the game immediately ends when you apprehend him. It is not known why the bomb situation was cut out, but it may have been due to memory or technical restraints. The Pegasus remake adds the bomb scenario as the final puzzle in the game.