Morana tells us that she has come to the underworld to help Yuji stay in the human race so that the reapers will no longer consume so much energy. This is a good reason for her to come, since she already knows that the first giver has left the earth. Yuji wants to stay in order to help keep the humans alive, so she has to leave. This seems like a good idea to us, since we already know that Yuji has left. But we don't really know what to make of it, because we're not really sure what's going on.