Last year, shortly after the excellent James Bond film “Skyfall” was released, I asserted in a column that an anagram at the heart of the film suggested that a critical subplot had been left on the cutting-room floor. I received several e-mails asking why I hadn’t disclosed what I thought I knew. The answer is that I couldn’t explain the anagram without including several spoilers. Now that a year has passed since the U.S. opening (November 9, 2012), I suppose it’s time to explain what I meant. (Warning: Those aforementioned spoilers are below!)

You will remember that the plot revolves around the destruction wrought by Raoul Silva (Javier Bardem), a former MI6 agent who is angry at M (Judi Dench) for allowing him to be arrested in Hong Kong and then rot in prison rather than arranging an exchange. Now, everybody knows that Silva’s name is an anagram (“a rival soul”) -- but that’s not the anagram I mean.

The key anagram is the cryptic message Silva sends to M shortly before all mayhem breaks loose: “THINK ON YOUR SINS.” The language is so highly stylized that I was certain, from the time the words appeared on the screen of M’s laptop, that there was a message hidden within. In the car on the way home after the film ended, I was already scribbling anagrams on a piece of paper. But I couldn’t solve it, even with the help of the Internet Anagram Server, until I remembered three bizarre aspects of the movie. (Here are the spoilers.)

First, why on earth did the screenwriters go to the trouble of telling the audience that Silva had been arrested in Hong Kong and was thought to be still languishing in prison there rather than, say, transferred to the Chinese mainland, as a British spy likely would be? Second, why was Silva’s enmity toward M so intimate and full of moments of appalling grief? And third, why, after vowing revenge -- and spending the entire film seeking it -- did he find himself in the climactic scene unable to kill her?

These clues came together, and the anagram was solved:

THINK ON YOUR SINS

became

YOUR SON ISNT IN HK

Suddenly, it all made sense. Silva, thought to be in Hong Kong, was M’s son -- adopted, possibly, but undeniably her son. (Why adopted? Because otherwise we can make no sense of M’s comment to Bond that orphans make the best recruits. Yes, Bond was an orphan, but the poignancy and faraway gaze as M says the words tell us she is thinking of somebody else.)

Once we see that Silva is her son, the steeliness with which she sacrifices agents at the beginning of the film (including, we believe, Bond himself) becomes more fundamental to her character. She has been steely because that is how she survives the memory of what she has done. Without the knowledge that she let her own son rot in prison for the sake of the Secret Intelligence Service, her death at the film’s end seems more contrivance than tragedy.

Immediately after the film’s release, as audiences tried to understand the emotional weight of the final scene, there were whispers in the blogosphere that we were meant to believe that Silva was M’s son. But none that I have found mentioned the key clue: the anagram on M’s laptop.

That, then, is my theory of what was left on the cutting-room floor: The anagram was meant to be translated for us and the family connection between Silva and M made explicit. If the filmmakers have a response, I’d love to hear it.