Prologue
—Giuoco Piano is a subtle joke. It might sound like something music-related, but it actually translates as "quiet game" in Italian and is the first recorded chess opening.
—"How come Z insists on using these stupid riddles and puzzles?": lampshading Zugzwang's signature tic. It's part of his psychological makeup: he enjoys testing others just to see how smart they are.
—Remember: Zugzwang isn't a major crime lord like these guys. Like Moriarty, he's a consulting criminal: a planner and advisor who offers information, equipment, planning and support to the highest bidder.
—Greenfield rifles: play on the Enfield rifle.
—Muletese Falcon: play on The Maltese Falcon by Dashiell Hammett, the first hard-boiled private detective novel.
—I created Scarlet Letter out of the realization that I had so far not had any female antagonists in the series. Scarlet Letter's name is a reference not to the famous novel by Nathaniel Hawthorne, but to the practice of Puritans forcing an adulterous woman to wear a scarlet letter "A" as a mark of her sin. Scarlet Letter exposes the scarlet letters of others to further her own ends and is also known for her writing skills.
—Burt and Ernie's names are of course a reference to the famous duo from It's A Wonderful Life.
—"mein Geliebte": German, "my dear."

Part 1
—Slide Fortissimo belongs to Trombone2015. Green Screen belongs to his twin brother, mandolin15. Gingerroot and Decibelle Rose belong to DatPoneEnthusiast90. All OCs are used with permission.
—"Frabjous day...calloo! Callay!": reference the Jabberwocky poem from Lewis Carroll's Through the Looking-Glass.
—Baden Switch: pun on "bait and switch."
—"Is it Bob or Joe or Walter?...": lines taken from the Weird Al Yankovic song, Everything You Know Is Wrong.
—Music: Libella Swing by Parov Stelar.

Part 2
—"supercalifragilisticexpialidocious": reference to Mary Poppins, of course.
—Fancy Shmancy is an upper-class Canterlot noble only mentioned in the comics.
—"something nouveau, something passionnant...": French, "something fresh, something exciting." My headcanon is Fleur De Lis is Prench (French).

Part 3
—"Hey! You stole my waffle!": Get it? Because "waffle" sounds like "waifu," and Flash is accused of being a...ah, never mind.
—"Is everypony around here crazy?": Yes, Starlight, they are.
—"Didn't do it...lawyer bucked me.": paraphrasing a line from The Shawshank Redemption. The character Green is a reference to Red from the film, who is played by Morgan Freeman: the fact that Green is a purple-coated pony is a subtle joke, a reference to the absurdity of a character named "Red" being played by a black man.
—"You got a file?...You got a cake to hide it in?": reference to the popular trope of smuggling a file or similar tool to a friend in prison in a cake.
—Fourth wall humor. There's nothing like it.
—Ryuthela secundaria: an actual species of spider. Look here.
—The usage of the cardboard box and the famous "Alert" sounds are both references (and a less than subtle "take that") to the Metal Gear Solid games. The Guard even lampshades just how absurd the usage of a cardboard box as a stealth device in real life would be.

Part 4
—"Buy some apples...": a joke only a brony would get. In some brony sites, "Buy some apples" is used a censor for curses.
—Music: Yakety Sax, the theme to the Benny Hill Show, a British comedy show well-known for its absurd chase scenes.
—The chase sequence that follows was inspired by Scooby Doo and Looney Tunes episodes. Little fact: before I joined the brony fandom, I actually wrote Looney Tunes fanfictions on deviantArt for a little over two years.
—One of the challenges of writing the chase sequence was not making the Guards seem too incompetent. For example, in the hallway sequence, the sergeant was originally supposed to follow Cheese and Pinkie through the doors, but I cut that part because it seemed a bit too silly for a non-party pony to be able to pull off the visual gag.
—The banana peel gag actually has a factual basis. In early 20th century America, bananas were very popular, but because of the lack of anti-littering laws, people would just carelessly toss the peels onto the sidewalk. Over time, the peels would rot and become quite slippery. A fresh banana peel, however, is not that slippery.
—Pinkie using the party cannon's blowback to send herself flying is based off of rocket jumping in many first-person shooter games, particularly Team Fortress 2.
—"take chances, make mistakes, get messy...": reference to The Magic School Bus TV series: this was one of Ms. Frizzle's many catchphrases. (Please tell me I'm not the only one who remembers that show)
—"Cardboard boxes are stupid.": take that, Solid Snake.
—The explanation as to why Twilight can't pardon Pinkie and Cheese in their crimes was something that I added in when I realized that it was a potential plot hole that needed addressing. My headcanon for the Equestrian government is that, somewhat similar to the American government, it has separate city/state/federal systems and a system of checks and balances that prevent one pony from becoming too powerful, something that I feel the Two Sisters would have insisted upon.
—Starlight's letter is an element for an ongoing minor plot arc in the series.
—Rarity's Shadow Spade outfit is a reference to the episode Rarity Investigates, one of my favorite Season 5 episodes.
—"certainement": French, "certainly."
—Applejack quite literally "lampshades" the problem of leaving the Falcon out in the open.
—In French, Laurier de Montagne translates as "mountain laurel," a beautiful but highly toxic flower. Laurier's color scheme is based off of the flower.
—Note Scarlet's alarmed reaction when she hears Phillip's name, a testament to his reputation amongst criminals.

Part 5
—"...that escaped doctor looking for the one-legged pony!": reference to The Fugitive TV series.
—"...Jess Horsefeathers...": reference to Jessica Fletcher (played by Angela Lansbury), the star of the famous Murder, She Wrote TV series.
—Bumblebee and Prowl's names are taken from two characters from Transformers, another famous Hasbro franchise.
—The old "fake tunnel" gag, a staple of Road Runner cartoons for years.

Part 6
—Rarity unintentionally narrating the story is a throwback to Rarity Investigates.
—Flash's instincts have no doubt been honed by working with Phillip.
—Cheese's insistence on proper grammar is a reference to the Weird Al song Word Crimes, a personal favorite of mine.
—Universe note: motorized carriages, mostly electric or steam-driven, are a fairly recent invention in Equestria, similar to early 20th century models (think Ford Model T). They are mostly only seen in larger cities.

Part 7
—The idea of a suspect falling out a window and landing on a train car came from the Sherlock Holmes story The Adventure of the Bruce-Partington Plans.
—Pinkie pulls of Bugs Bunny-style reverse psychology on the thug to get him to reveal his secret.
—The little skit between the two thugs with the "secret lever" is a reference to the Deadpool video game.
—I thought it'd be funny if awkward elevator music was playing while Pinkie was descending into the secret hideout. It'd probably be funnier if this was a movie and not a story.
—hoping that they had reorganized since the last time she was there: reference to a previous story, The Blue Moon Brings Death.
—For Pinkie's fighting style, I took inspiration from the Afro-Brazilian martial art of capoeira. As much a dance as it is a martial art, capoeira is highly acrobatic and uses constant movement and fast kicks, perfect for the highly energetic Pinkie Pie.
—"Crétins incompétents!": French, "Incompetent morons!"
—"Bien sûr": French, "of course."
—The ending and the music in the Author's notes are both references to the famous "game over" sequences from the Metal Gear video game series.

Part 8
—"Say hello to my little friend!": reference to Scarface.
—"My leg!": reference to a running gag from Spongebob Squarepants.
—Pinkie's Pinkie Sense saves her once again.
—"You're despicable,": copying one of Daffy Duck's catchphrases.

Part 9
—"And I would've gotten away with it, too...If it weren't for you meddling ponies!": reference to the Scooby-Doo series, where the villain would always state at the end that they "would have gotten away with it, if it weren't for you meddling kids!" or some variation thereof.
—"Hidden beneath our bed,": in the very last place any thief would think of looking.
—Of course I was going to have Cheese and Pinkie kiss at the end. What, did you think I wouldn't?
—In an original outline for the story, it would be revealed that Phillip had lied about having to go to Vanhoover and had actually been following the group since the beginning to keep an eye on them. I cut this idea as both unnecessary and because I didn't really have a good reason for Phillip to do that (or at least, none that ended up with him not seeming like a jerk at the end). What I wanted to convey with this scene is the idea that Flash is growing up to be Phillip's peer and equal, and that Phillip is learning to trust his friends.
—"I'd better find a place to hide.": Phil was in Ponyville the last time that Cheese and Pinkie planned a party together. It's not an experience he'd like to repeat.
—For the record: no, they're not going do anything past kissing and cuddling. Both Twi and Flash have agreed to wait until marriage to give away their virginity.

Epilogue
—Scarlet and Laurier have managed to escape justice, but may have jumped out of the frying pan and into the fire.
—Question: why did Zugzwang use this convoluted method to take control of the Scarlets instead of just killing Scarlet Letter? Answer: because killing her and just taking over would have made all the Scarlets his enemies. This way discredits her and puts her into his debt, as well as focuses her concern on her family and her son.
—What's Zugzwang got in the bag? What's he got planned? He'd tell you, but then he'd have to kill you. No, seriously.

Author's Notes:

Chapter notes from the story.