The story of Drake and Elena's relationship was this:
The game starts with Drake working with Cutter, Chloe and Sully. There is no mention of Elena, and when they realize they need her help, Drake is very against it, implying that yet again, the relationship didn't work out.
Later on, we see them together after the ship incident, and Nate mentions her ring, implying that they were engaged. We also see why they are apart at the moment, with how Elena can't handle Nate's obsessive nature with these treasures.
It isn't until the very end in the scene with Sully that we see Nate has a ring and they were in fact married, after all, men don't wear engagement rings.
So the natural conclusion is they got married before Drake's Deception and then separated and after the game, they made up and settled down.