For those of you who need clarification *spoilers* this is a summary:
So Ed bought a new place to stay in Central, but while he was checking it out before the purchase, Roy was in the apartment in stead. Lying about his reason for being there, Roy claimed that he too was looking for a new home for purchase. Although in the beginning Ed wanted the place for residence, it soon became the rendezvous point for sexual liaisons with Roy, ones which only sterilized their understanding of one another and rendered them both anonymous sex friends with no hope for furthering the state of things. Ed's new apartment became a symbol of their new, corrosive status.
And then one day Ed realizes that the chalk and chalk marks he's been seeing around the apartment are actually the remnants of a transmutation circle. It is implicit from the context that we assume this was a human transmutation circle. And sure enough, Roy concedes under pressure that he was the apartment's original owner, and he had drawn the transmutation circles during his wartime tour and presumable afterward as well. Afterward we can gather that he was lying all along about his reasons for being present that day in the apartment, at the same time as Ed.
Enraged and hurt and upset even before hand at the disgustingly toxic relationship they'd been kindling, this new information about Roy leads Ed to finally realize the extent of the damage "the room (symbolically, their relationship)" was inflicting on both of them. He forcefully has sex with Roy, by this time noticeably listless during many sexual encounters and possibly still suffering from PTSD.
Ed, scared that he knows all too well the baggage of the memories that Roy has seen, draws away from the relationship completely and decides to cut things off. He ask Roy for the other set of keys to the apartment. And after that, they act as though nothing had every happened between them, as if they sealed everything away in that room.