I think he wants to become a hero, and maybe he is somewhat listening to good old dad when he said if Gideon kills Emma he will never become the hero he wants to be. I would hope that Emma would help him she is supposed to be the savior. The problem is, that Emma is a “hero” on this show and the heroes tend to think in black and white. They see Gideon as a villain so won’t trust him and unless the black fairy becomes a problem for Storybrooke Emma may say not my problem. I hope not though. I think it would be great if everyone teamed up against the black fairy if she is as bad as we think she is.
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