The title and plot of the episode reference the 2006 film The Departed. The episode contains several elements of the film, including the use of the Dropkick Murphys song "I'm Shipping Up to Boston", the chasing scene and the ending, which shows a rat.
The Dropkick Murphys song "I'm Shipping Up to Boston" is heard when Bart and his friends play jokes on Skinner and when Bart is chasing the rat. This song gained worldwide attention for its use in The Departed.
Lisa contributes to the NPR (National Public Radio) by putting a coin in the car stereo.
The voice of Terry Gross, who is the host of the famous interviews program Fresh Air, is heard when she introduces a 1987 interview with Senator Alan Cranston.
Before the Diet Coke and Mentos eruption reaction happens, Skinner says "sorry to plop plop on your fizz fizz" while confronting Bart. "Plop plop, fizz fizz" is the catchphrase of Alka-Seltzer.
At the end of the episode, Ralph states "The rat is a sign of obviousness." He then smiles slightly, hinting that Ralph may have been the one true Rat.
After Principal Skinner locks Bart and Donny in the detention room, he chuckles to himself, but his mouth doesn't move.
When Bart found out that that Groundskeeper Willie is on Principal Skinner's side as a rat, Bart's lips saying "Willie? You're on Skinner's side?" were out of synch.