Basically my idea is that, when Madi chooses not to come back, she chooses somsone to come back in her place, and she chooses Bellamy. (Who cares if he didn't transcend? None of the plot makes sense anyway.) So Clarke sees all her so-called "friends," then sees Bellamy. She apologizes to him and he gives her the "If you need forgiveness, I'll give that to you," line again. Then they AT LEAST hug, and it ends with them looking around and her asking, "What do we do now?" and he of course responds with, "Whatever the hell we want."