- Many to Homestuck, with some crossing into full Homage. Muir is open about having written Homestuck fanfiction in the past.
- Gideon the Ninth, and consequently, the series, begins with a young woman in her bedroom.
- The books are dedicated "to pT." pT is paraTactician, Muir's life partner. It's a safe assumption that they met writing fanfic.
- Muir openly states that Matthias Nonius is named after a character from Redwall.
- The Emperor quotes poetry often, including The Little Mermaid, "Annabel Lee", and... Evanescence.
- Harrow says (as do the House posters put out by Tor) that the Seventh's weakness is "a fatal longing for the picturesque", a slight paraphrase of the protagonist's assessment of his fatal flaw in The Secret History.
- When revealing the Sleeper's true name, we get a triple Shout-Out:Commander Awake Remembrance of These Valiant Dead Kia Hua Ko Te Pai Snap Back to Reality Oops There Goes Gravity
- "Awake Remembrance of Those Valiant Dead" is from Shakespeare's Henry V.
- "Kia Hua Ko Te Pai" is a line included in the Maori language version of author's native New Zealand national anthem.
- "Snap Back to Reality Oops There Goes Gravity" is a lyric from Eminem's "Lose Yourself."
- Part of Muir's authorial style includes incorporating meme references into the text, often ones that were popular only on Tumblr, which she has acknowledged doing because she finds the contrast funny.
- Harrow snarks that "While we were developing common sense, [Gideon] studied the blade." In the same sentence, she notes that Gideon is good enough with a sword to be able to wield a sword in each hand and one in her mouth.
- Muir's notes on Dulcinea's name finish with "In this essay I will"
- The Emperor notes that he's protected from the Resurrection Beasts to prevent the Nine Houses from becoming "none House, with left grief."
- When fighting the Heralds of the Resurrection Beast, Gideon apologizes to Harrow for getting her thumb bitten off, but says, "[...] these motherfuckers had a hunger that only thumbs could satisfy [...]"
- Gideon's final spoken lines in Harrow the Ninth are "Jail for Mother."
- Harrow the Ninth includes a reference to Homestar Runner of all things, when Ianthe compares Harrow to a puppy "with three legs missing insisting you can make it on your own".
- Ianthe's abbreviation of "Harrowhark" to "Harry" is one to Harry Potter, and to Ianthe's intended Draco in Leather Pants status, according to the author.
- At one point, Harrow asks Dulcinea why she wants to be a Lyctor. Gideon then mumbles that she can't just ask people why they want to be Lyctors.
- Ortus and Sister Glaurica literally died on their way back to their home planet.
- At one point, Mercy quotes a viral Reddit Post, wherein an overly entitled woman demands help and then refuses all offers as inadequate.Mercymorn: It's a Resurrection Beast, honey! Thank you, next!
- The scene in Harrow the Ninth where Ianthe and Gideon argue over their feelings for Harrow and Gideon says that Harrow doesn't love her because Harrow only loves the Body is eerily reminiscent of the scene in Lost Teeth Like White Jewels (which is one of Muir's fanfics), where Sollux tells Eridan and Gamzee that Karkat can't really love any of them no matter how much they love him because he only loves the Threshecutioners.
- Similarly, after Harrow applies Gideon's face paint for the first time, Gideon's only comment is 'I look like a douche', which is almost exactly what Terezi said in The Serendipity Gospels (another one of Muir's fanfics) after she first let Gamzee put face paint on her.
- In Harrow the Ninth, Gideon lists off some regrets, including "not kicking Crux down a flight of stairs and watching him go ''Oof, ow, my bones'' down each step ..."
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