This idea was brought up in the chat. Does Emma know that Milha was Bae’s mother? My guess is that she doesn’t know that fact or what Hook did to Bae. And I don’t think Hook would volunteer that information. I think Neal will be the one to inform Emma that Hook took his mother from him as a child and destroyed his family. That might be another thing that makes Emma think twice about kissing Hook again when she discovers Neal is alive.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy