In order to not give spoilers, I will try to talk very generally.
There are various actions you're supposed to do within the game that are now impossible. The problem is that they rely on special timing within the AITD2 code. Modern computers are so fast that the timing routines no longer work, and these actions are not doable by computers that use a processor faster than a Pentium II. Therefore, you can not finish the game on a modern computer without resorting to slowing down your processor.
There are various utilities you can obtain via Google to slow down your processor.
Datapoint: On an AMD 1.3GHz Athlon, I had to slow my CPU down to about 40% before the actions became doable. One of the very first puzzles in the game is one of the undoable ones, so you should know right away whether you'll be able to finish the game or not without slowing down your CPU. Add
Did You Know?
When Carnby dies, the haunting music that plays in the background is "Vesti la Giubba" from the opera "I, Pagliacci". Add