Maggie is taken in by a convent of nuns, who need an innocent child to solve an ancient religious 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.

* TheChosenOne: 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).
* DarkMessiah: The moment Bart comes to the cathedral and sits on the throne Maggie used to occupy, the world literally goes to hell.
* DontExplainTheJoke: Homer basically spells out they are making a ''WesternAnimation/{{Ratatouille}}'' reference before actually making it.
* FoxChickenGrainPuzzle: With Santa's Little Helper, Maggie, and rat poison. Cletus has a fox, duck, and corn (before he notices, the corn is eaten by the duck, which is gobbled up by the fox).
* GilliganCut: Homer insisted he wouldn't dress himself as a nun. Cut to the next scene and he's [[SubvertedTrope still wearing his everyday clothes]] while Lisa was disguised as a nun. Then he asked her if she's really sure she doesn't want him to do it. [[DoubleSubversion He put on a nun disguise]].
* TheKindnapper: Considering the case Homer [[NotHelpingYourCase was building]] to persuade the nuns to let him take Maggie back, can anyone blame them for keeping her?
* ShoutOut:
** The title of this episode is parody of the movie, ''Literature/GoneBabyGone''.
** The scene with Sister Marilyn parodies [[MarilynManeuver Marilyn Monroe's famous dress-blowing scene]] over a subway grate in ''Film/TheSevenYearItch''.
** Mr. Burns' quips "Tardy Boys" and "Nancy Clueless" are references to popular children's mystery book series The Hardy Boys and Nancy Drew.
* SmallNameBigEgo: Lisa, when she gets the wrong answer telling her she's TheChosenOne.
* WholePlotReference: The main plot of this episode spoofs ''Film/NationalTreasure'' and ''Literature/TheDaVinciCode''.