In a parody of The Da Vinci Code and National Treasure, Maggie is abducted by nuns, who believe she's the fulfillment of a mysterious religious prophecy, while Principal Skinner, Comic Book Guy, Mr. Burns and Lisa also try to solve puzzles related to the mystery. Meanwhile, Marge goes blind from staring at a solar eclipse without a pinhole projector and Homer tries to cover up Maggie's disappearance before Marge can gain her eyesight back.

Tropes in this episode include:

• Ancient Conspiracy: As a parody of The Da Vinci Code, this naturally figures into the story.
  Mr. Burns: You see my dear girl, I joined the Freemasons before it was trendy. That's my eyeball on the dollar bill. That's also my pyramid.
• And I'm the Queen of Sheba: After the head nun angrily tells Homer that she's married to Jesus, Homer sarcastically replies that he's married to Wonder Woman.
• Arson, Murder, and Jaywalking:
  • Lisa objects to Marge taking Maggie away from the throne, because "she's brought peace to our town! And reports of less road rage in Shelbyville!"
  • Comic Book Guy noting that "legend and Wikipedia have it that the gem will be revealed during the first full moon after a solar eclipse."
• Boats into Buildings: In a flashback, the band of nuns sail to the New World on a ship which they flip over to use as their convent.
• The Chosen One: Maggie. Lisa, after going through a very long Da Vinci-like series of puzzles, comes across an anagram puzzle that seemingly tells her she's the one (Regally, the rock gem is Lisa), and brags to the nuns about the fact, until the head nun corrects her anagram to an insulting correction (It's really Maggie, Sherlock) that reveals Maggie is the one (which Lisa points out only works after reading the first incorrect anagram).
• Clueless Mystery: Lampshaded; over the course of the episode the audience is presented with three riddles to solve, but while the first two are solvable by the viewer (in fact, the first is the classic Fox-Chicken-Grain Puzzle), the caption of the third, an anagram, asks the audience if it wants to "try" to solve the riddle while admitting, "We can't." The actual answer is phrased as a rebuke toward Lisa's failed first attempt.
  Lisa: You know, I have to point out that this only makes sense if I get the wrong answer first.
• Continuity Nod: Lisa mentions kissing Milhouse, probably referring to "The Last of the Red Hat Mamas." Just like in "Lisa's Wedding," it doesn't count.
• Dark Messiah: The moment Bart comes to the cathedral and sits on the throne Maggie used to occupy, the world literally goes to hell.
• Disproportionate Retribution: A janitorial nun tips off Lisa about the Mystery of the Legendary Gem just to spite the head nun who always hogs the quarterback role whenever they play football.
• Don't Explain the Joke: Homer basically spells out they are making a Ratatouille reference before actually making it.
• Downer Ending: Marge robs Springfield, and the world, of a new era of peace by denying Maggie's right as The Chosen One. What's worse is that Bart is left behind who's presence as a Dark Messiah brings about (in this episode at least) the literal end of days.
• Eye Scream: Marge goes blind for two weeks because she looked at the solar eclipse without the pinhole projector (she gave hers to Homer because his broke).
• Fisher King: As soon as Maggie is placed on the throne, Springfield experiences vast levels of harmony and goodwill. But when Bart takes the throne, everything changes into a literal hellscape.
• Fox-Chicken-Grain Puzzle: "How does the fool cross the river with his burdens three?" The fool being Homer, with Santa's Little Helper, Maggie, and rat poison. Homer figures out a way to solve his puzzle and is so focused on it that, when he sees Santa's Little Helper swimming, he berates the dog for not paying attention to his plan. Then Cletus has a fox, duck, and corn (before he notices, the corn is eaten by the duck, which is gobbled up by the fox).
• Gilligan Cut: Homer insisted he wouldn't dress himself as a nun. Cut to the next scene and he's still wearing his everyday clothes while Lisa gets ready to infiltrate the convent herself. Then he asks her if she's really sure she doesn't want him to do it and puts on a nun disguise.
• Good Hurts Evil: Downplayed. Burns is convinced into escorting Lisa and the Tardy Boys to the church to usher a new era of peace. After Smithers asks how it feels to do something good, Burns negatively replies that it feels gross.
• Gut Feeling: In spite of her blindness, Marge was able to make her way to the church to take back Maggie based on her motherly intuition.
• The Kindnapper: Considering the case Homer was building to persuade the nuns to let him take Maggie back, can anyone blame them for keeping her?
• Naughty Nuns: Sister Marlin has a habit of showing her good stuff, unlike the other modest sisters.
• Riddle Me This: Lisa tries to solve a series of riddles related to an ancient conspiracy to find out where Maggie is.
• Rube Goldberg Device: Whoever was in charge of designing the contraption behind the church's organ piano really went all out with it's contraptions and set up. Lisa ends up waiting a good hour or so before it can give her the next clue.
• Running Gag: The puzzles being provided before the ad breaks.
• Shout-Out:
  • The title of this episode is parody of the movie, Gone Baby Gone.
  • The scene with Sister Marilyn parodies Marilyn Monroe's famous dress-blowing scene over a subway grate in The Seven Year Itch.
  • Mr. Burns' quips "Tardy Boys" and "Nancy Clueless" are references to popular children's mystery book series The Hardy Boys and Nancy Drew.
  • When the 16th century nuns arrive at the future site of Philadephia, they're greeted by the Phillie Phanatic.
• Small Name, Big Ego: Lisa, when she gets the wrong answer telling her she's The Chosen One.
• Stern Nun: The Mother Superior, also a Deadpan Snarker.
• Surprisingly Realistic Outcome: Homer manages to solve the classic Fox-Chicken-Grain Puzzle, but fails to gain the desired result when he puts it into practice as leaving the commodities (in this case Maggie) unattended on the opposite riverbank causes its own problems. He probably also should have expected that Santa's Little Helper (the "fox") would try following him across the river upon being left on the bank.
  Homer: Were you listening at all?!
• Total Eclipse of the Plot: The Legendary Gem is said to be revealed on the first Full Moon after a Solar Eclipse.
• Whole-Plot Reference: The main plot mixes elements of The Da Vinci Code (an Ancient Conspiracy involving the Catholic Church, based around puzzles and a MacGuffin) and National Treasure (a conspiracy dating to Colonial times, with The American Revolution as part of the conspiracy).
• Younger Than They Look: The janitorial nun who helps Lisa warns her that in spite of her hag-like appearance, she's actually 23.