The Deck of 52 is the codename given to the 52 people that the Allies note as the most dangerous ones. It is modeled after an American deck of cards, complete with each person being assigned one of the cards in the deck. The face cards (Jack, Queen and King) are a part of the contracts for the various factions, while the Aces are part of the big missions at the end of each suit.
The rest of the Deck of 52 are hidden throughout the map, and have to be found and captured/killed on your own time. As you complete contracts, you will get e-mails as rewards that tell you the general location of where each one is located. Note that you get the full amount if you subdue them and capture them alive, but you only get half that if you kill them. You will have to call in the helicopter to pick them up after subduing them. Also note that after getting the Ace of a suit, you will not be able to go back and get any other card in that particular suit.