How interesting, I have started to write an FAQ regarding this game. I'm about half-way done though.
Anyways, with the last level...I think I know where you are stuck.
If you are in the room right after you go up those two flights of stairs, there should be a door to the right of those stairs (look at it as you are going up the stairs, then take a right.)
The door is in the shadows, so just click the X button or whatever when you see the (!) symbol.
Once you are there, there will be many guards in many different rooms. Kill them all but be careful. There will be some hiding behind the couches and in other rooms to where they might sneak up behind you.
Once you go through all these rooms, you will hear Tom call out Sam's name. Follow him and then finish the level.
-Hope this helps.
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