Infiltrator

The players must pretend to be bad guys, infiltrating an evil organization in order to bring it down. This could be a more military/covert mission like getting inside the IAS, or it could be a more social infiltration like with the Witan or ROME. 
This story could also be even more specific: the main characters have been tricked or hurt by a covert agent, and now they want to track them down and bring them in. Imagine how hard it would be for the characters to infiltrate the Order of Serpents, who are themselves natural spies and spy hunters.