I'm going with: During that whole ocean-storm fiasco, Makoto was too late to rescue Rei. He returned to shore to a weeping Nagisa to tell him the heartbreaking news. His beloved Rei-chan would never be coming back.
I'm going to say that in this pic Rei actually died... (he better not but a lot of people think he's going to... and a few signs point that he might! TT^TT I would be super sad if he did because he's my favorite character and I ship him with Nagisa...)