Kill your target in Mission 2, or alternatively (nonlethal):
Knock him out and carry him to the interrogation room to brand him. If you are going for the bodyguard achievement as well, you'll need to follow the two men into the basement prior to knocking the Overseer out (this way is a bit harder, but gets you an extra achievement). You will also need to grab a key to the room from a guard nearby (usually in the file cabinet room). Put the Overseer in the chair, grab the brand from the balcony, and then use it on the Overseer.