He does get a little defensive: “that’s my story and I’m sticking to it” despite the fact that he’s always been the one to harp on her super power.
Now, I don’t think he’s lying to be malicious or because he’s working for Zelena. I think he knows all about Neal and is trying to keep it under wraps at the behest of Neal himself. But he could at least acknowledge that she’s right, he’s lying. Isn’t something that Anti SFers say is that Neal doubts Emma’s superpower from SBandT
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"He was a lot of things to me" "The only conclusion was love"