Why do the machines keep humans alive if they have nuclear reactors? There are several factual inaccuracies here. "The Matrix" isn't near Zion, they need to use ships to get to and from places where they can hack in to the Matrix. The plan for the attack in the last movie was for them to wipe out Zion, the Architect says as much.
May 8
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How did the bad guy actually die? Tony waited until the full suit was on Killian (including the helmet) before blowing the suit. His entire body had cracks in the surface afterwards, as it was all healing/regenerating.