Emma is the one keeping the secret from Hook, not the other way around (though he does have many skeletons in his closet still). Her secret is probably having shaking hands like Aladdin and fearing she’s cursed to live alone due to being the savior.
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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