There will be unmarked spoilers. You Have Been Warned.
The Court Founders and Jeanne
- In Chapter 1: The Shadow And The Robot, Shadow 2 tells Annie that the Annan Waters are dangerous, but isn't able to tell her why. It's because of Jeanne, as revealed from Chapter 8: Broken Glass And Other Things onwards.
- In Chapter 12: Mainly Involves Robots, Robot tells how he had a new arm grown for him. Tom comments at the bottom of the strip that "It all begins with a seed." which takes on a deeper meaning now that we know he was describing the entirety of Gunnerkrigg Court, as Chapter 44: Crash Course shows.
- In Chapter 18: S1, Tom, once again, makes a snarky comment about someone, this time it's Diego. ("You see he probably had a good personality") Cue Chapter 25: Sky Watcher And The Angel, where it's revealed how much of a good guy Diego was.
- From Chapter 20: Coyote Stories: "There were some humans and creatures living on both sides. Many of the current inhabitants are descended from those humans". That's an interesting last panel — and, as of Chapter 30: The Coward Heart, a careful phrasing, as it turned out.
- Chapter 24: Residential has the Laser Cows, the resident workers of Young's Park, who refuse to cut the grass near the monument to Sir Young, founder of the Court. Cue the next chapter where it's revealed that Diego despised Young himself for his plan in order to lock up Jeanne in the Annan Waters; the robots of the Court -many of which, such as the aforementioned Cows, work in the aforementioned area- may have inherited this same feeling.
- In Chapter 6: A Handful of Dirt Kat assures Annie that the school would surely know where her father was. Why, yes. Yes, they did.
- At the end of Chapter 14: The Fangs of Summertime, Annie said "And so did I wait for word from my father, unaware that I would not hear from him for over two years." This only sounds like a simple reveal until it turns out, in Chapter 37: Microsat 5, that she quite literally meant it, that her father only calls her, that she would only "hear" his voice over the phone.
- The end of the first book shows a rocket being launched, and Tea and her partner watching it through a telescope. Cue Chapter 37: Microsat 5 and it's actual rocket launch, 700 pages, 2 in story years, and several real life years later.
- In Chapter 18, when Reynardine is showing concern about Annie, Kat says "Were did this come from? Are you her dad in disguise now?", and Reynardine replies "Ugh, perish the thought." It sounds like he's just downplaying the idea he might feel parental towards her, but we later learn he knows Anthony and has reason not to appreciate being compared to him.
Annie's heritageThere is quite a bit leading up to The Reveal of Chapter 31: Fire Spike:
- Chapter 3: Reynardine introduces us to Renard himself. At one point, he recognizes Annie as Surma's daughter, and is sad when he concludes that Surma is dead.
- In Chapter 18: S1, at some other point, in a flashback, the one who is sad is Anja, after reading Annie's transfer letter.
- In Chapter 20: Coyote Stories, Coyote tells Annie of the origins of both the Court and Gillitie Forest. At some point, he says "There were some humans and creatures living on both sides. Many of the current inhabitants are descended from those humans". It turns out that Annie is a descendant from a fire elemental.
- From Chapter 21: Blinking, page 28: "The day Surma died, none of us came for her." and "I had to do it myself."
- From Chapter 23: Terror Castle of the Jupiter Moon Martians, Renard does a comment towards Annie: "You have a fire in you, child, a fire that belonged to your mother!". This turns out to be a Literal Metaphor.
JonesAlso regarding Jones' nature, revealed in Chapter 40: The Stone, there's quite a few hints scattered around:
- Chapter 14: The Fangs of Summertime : while discussing Ysengrin's new body, Jones mentions that she's never seen anything quite like it. The Headmaster notes that it's a disturbing sentiment coming from her of all people.
- Chapter 17: The Medium Beginning has her deflecting a sword with her face and Eglamore saying that she would flatten him at close range.
- Chapter 23: Terror Castle of the Jupiter Moon Martians has the group transported from the simulator to Parley's bed. Take notes on how far each person's feet sink into the mattress.
- Chapter 28: Spring Heeled, Part 2 has her destroying the binding program holding Renard with her bare hand, coming out of the water unscathed, and using her bare hand to make a hole in the concrete. Renard also comments that she is a little touchy about her weight.
- At the end of the same chapter, Renard calls Zimmie a demon, and Jones gently rebukes him, calling it "A label commonly applied to what is feared and misunderstood." Later on we learn that Jones herself was accused of being a "devil" by superstitious medieval folk.
- Chapter 39: The Great Secret has Coyote explaining that mythical beings such as himself are created from the minds of humanity, Annie objects that it doesn't explain Jones.
- There is a plaque on the wall of the hallway Mort haunts reading "Dulce et decorum est". This is a reference to the poem of the same name by Wilfred Owen, a young poet who was killed in World War I, and is about the horrors of war and the needless deaths of young men. It becomes relevant in Chapter 47, when it is revealed that Mort was killed in a bombing during World War II when he was a young boy. After Annie guides him into the ether, the full plaque is seen on a page entitled "Pro patria mori", another reference to Owen's poem.
- In Chapter 5, Kat is upset that no one is paying attention to her gravity field generator; she later uses it to build a hovercraft to rescue Annie from the Annan river in Chapter 8: Broken Glass And Other Things.
- Renard's complaint that he cannot possess a new body unless Annie orders him to. This was a convenient leash, as of Chapter 52: Sneak, since Annie's remaining self-confidence was still enough to transfer him to Kat instead of her dad.
- In the bonus page of Chapter 11: Dobranoc, Gamma, Zimmy wants to chase spiders. Cue Chapters 27 and 28: Spring Heeled, where it's revealed why they need to be chased down.
- Chapter 27: Spring Heeled, Part 1, where Jack casually mentions to Annie that the information about the Chester and Foley students being blocked off. Later, in Chapter 34: Red Gets a Name, Jones mentions to Annie that the Court don't follow the activities of both houses on purpose.
- Chapter 39: The Great Secret has Eglamore advising Annie that the Court isn't liking the way she's behaving. Cue Chapter 41: Changes, and it turns out that Antimony hasn't been chosen as the new medium of the Court.
- Chapter 40: The Stone: one of Jones's flashbacks involves her surviving a bombardment in WWII era. Little did anybody know that, come Chapter 47: See ya!, someone else died that day: Mort.
- In Chapter 36: Red Gets A Name Annie visits the Foley kids and learns Ayilu can alter people's memories and make them believe whatever she wants even if they're aware it can't be true. In Chapter 58: A Big Day! we get reminded of this power and in Chapter 59: Jeanne Annie recruits Ayilu to help her free Jeanne by basically doing an Inception: Ayilu is the "architect" creating an imaginary Court for Jeanne to live in and populating it with literally Faceless Masses while helping Parley, the "forger", play the part of Jeanne's dear friend.
- The Court adults repeatedly brush off concerns about Ysengrin's aggression on the grounds that Coyote barely acknowledges Ysengrin's existence and would never grant him the level of power he seeks; however, in Chapter 66, he does just this, and Ysengrin eats him.