I am assuming that you cant get out of the citadel to carry on with the story line... getting to act 2 including the act 2 battlefields
The keys you found when you killed samuel's guards, will open a door that was previously locked.... leading to the exit (a slight way west from where samuel was)
There are other ways to get out too.... by mixing salt and sulpher and putting it in the forge (you also find the key for this by killing the guards by samuel)...
The salt you can find on prison level 1 (where you killed fergus), the sulpher you find by the doctor on the baracs levels.
Hope this helps you <img src="/ubbthreads/images/graemlins/smile.gif" alt="" />
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