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It wasn't when Emily died that JJ realized it. It wasn't when she was revived either, nor when the decision was made to keep that truth a secret. It wasn't when JJ stood face to face with her colleagues and grieved a grief so different from their, so much lighter and dirtier. It wasn't then that she realized it, and it wasn't even when she saw Emily sitting outside that café in Paris, looking so different and so much the same.
It was moments later, when Emily got up and left her behind at the table with the untouched glass of wine, that JJ realized that she didn't love her like a sister. That she didn't love her like a friend. That she just, simply, loved her.
