Question: In the very last scene, we see Michael Shannon in shackles (presumably in a federal prison) with electroencephalographic sensors attached to his forehead and scalp, oddly gazing at the sunrise as two prison guards flank him. In the very last shot of the film, a closeup of his face, we see his eyes faintly glow for a split-second as he smiles a very slight smile. Question: Is the film implying that Alton is in otherworldly contact with his father, or that his father absorbed some of Alton's otherworldly power; or is it implying that, being the boy's biological father, he was the source of Alton's power? In any event, this may never be revealed, because the film barely made back one-third of its $18 million production budget, making the probability of a sequel highly unlikely.
Answer: I wasn't sure what to make of it, but I got the impression that he was communicating with Alton like he had done when Alton ran from the truck. I also thought his smile was perhaps in reaction to what Alton told him and/or the two were making fun of (mocking) the use of electrodes because they knew the electrodes would not have any effect on him.
P.S. Plenty of lousy movies have had sequels, so it is possible there could be a "Midnight Special 2".
Not necessarily holding my breath.
A sequel doesn't seem likely. Hope you weren't holding your breath waiting for an answer to your question.
Answer: They did recognize each other (at one point he goes to her house without asking her address). After the divorce, Howard said that he wished they were strangers again. They literally behaved as if they never met each other before (even though Madeline is gently pushing to move past being strangers - for example, by guessing he's divorced).