Completely agree with Socomama's plot hole issue. This episode stood out to me as INSANE because the writers clearly wanted to stay focused on the 'almost-first-date' romance plot. The first thing we hear Clark say about Luthor is that 'long fall from a penthouse' when they're in the sewers. The first thing we hear is a wise-crack? For Superman's arch-nemesis and the one person to nearly separate Lois & Clark? So weird! So glad you're taking a more realistic look at this!

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Dr. Hamilton brought back Bonnie and Clyde and their gang from the dead. Superman brought you back from the dead! I think this brings us to the logical conclusion that people can be brought back from the dead.
I just love a solid TOGOM reference!

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And I would have stayed, his mind supplied. If not at her apartment, outside of it, all night long.
Aww, that one really hit me.

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Luthor managing to come back from the dead just in time for their first date was almost Shakespearean.
Yes! And finally, a reason why the pieces of the Phoenix episode make sense!

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“Lois,” Perry cut her off, putting a hand on her shoulder. “This man nearly destroyed the Daily Planet for good. It’s either Clark, or we can talk to Henderson about hiring some extra security—your choice. Just until Luthor is no longer a threat.”
This is a great point! At least Perry has some sense!

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Clark wondered if he would ever be able to tell her how she alone possessed the unique ability to render Superman vulnerable with just one look.
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This is doing an awesome job of marrying together information that the show gave us, which the characters seem to forget on their week-to-week adventures. It's also pulling Clark straight back to the end of season 1 mentally, which really feels like a trauma response. So interesting to see!