The Deck of Cards is an object that was important to the Order as it was used in their rituals. If the faces of any of the cards are shown to a person, they experience a violent vision involving either the Event or the Conroy Experiment (maybe both but more likely the former).
The Deck was stolen from the order by Martin Ruber along with the Watchbox, and was used on Lee Bridgewater and several policemen to free Joe Miller from the Police. Martin attempted to use it on Joe after he was allowed in The Room so he could steal their Objects, but it did not work since they were inside The Room. Joe then took the cards from Ruber and cast him out of the room and into a desert. In Ruber's case, the hallucinations he experiences when the cards are used on him include visions of him killing Lou, his former friend. It is possible that the cards simply make their victims relive their worst memories as well as seeing visions of the Sunshine Motel and the Objects.
The Cards presumably either stayed with Joe or went to what was left of the Legion.