The core book consists of a fictional novel, Ship of Theseus, written by a fictitious author, V. M. Straka, whose exact identity is unknown. It tells the story of an amnesiac traveler named "S", who tries to figure out who he is. In his travels he finds himself aboard a mysterious ship and then being involved in a conspiracy.
The novel is accompanied by footnotes from an equally mysterious editor and translator, F. X. Caldeira, who, curiously, has never met Straka face-to-face.
Additionally, the book's margins are filled with handwritten notes by two readers: Eric (a graduate student and a long-time Straka scholar who got kicked out of the university) and Jen (a senior student working in the university's library). The two start passing the book between each other. At first, they discuss the novel and try to discover the real identity of Straka and Caldeira. Eventually their relationship deepens and soon they become involved in their own conspiracy related to Straka's identity.
Lastly, there are physical inserts in the form of letters, postcards, maps, and newspaper clippings, left by Eric and Jen.
This book provides examples of:
- Anachronic Order: The marginalia are scrambled through the novel, even the ones with the same color.
- Animal Motifs:
- Ilsa frequently uses bird themes in her academic essays to the point of obsession.
- Many of the characters Eric and Jen discuss have bird names, usually in foreign languages. Some names translate as or refer to "magpie", "eagle", etc.
- When Eric goes to Brazil to find Caldeira, he uses birds as a secret code language on his postcards to let Jen know how he's doing with finding Caldeira; he refers to Caldeira as "the Nightingale" or "the rare bird" and writes things like "they heard [the bird] sing".
- The monkey is also frequently seen and mentioned in the book's text, usually coinciding with important plot points.
- Brain Fever: Eötvös Syndrome, a fictional disease that causes disorientation the closer one gets to the equator.
- Breaking the Fourth Wall: Eric and Jen are wondering what the potential reader might think of them in case the book and their notes are discovered by someone else.Jen: You're funnier since the sex.Eric: Eh... weren't you concerned that people might read this?
- Caps Lock: Eric always writes in all upper case letters. It doesn't come across as shouting though because his handwriting is smaller than Jen's (making it more of a case of "small caps", if such a thing would exist in handwritten text). This is probably done on purpose for the reader to more easily differentiate his handwriting from Jen's.
- Color-Coded for Your Convenience: The marginalia have different colors indicating both the author and the time during which they were written:
- Gray pencil is first used by Eric when he wrote the comments during his first reading when he was a teenager.
- Blue (Jen) and black pen (Eric) when they begin passing the book between each other.
- Orange (Jen) and green pen (Eric) after their relationship becomes more personal.
- Purple (Jen) and red pen (Eric) after the two have met in person.
- Black pen (both Jen and Eric) after they moved together to Prague.
- Feelies: Several inserts are wedged between various pages of the book by Eric and Jen, ranging from items concerning their bid to uncover the mysteries of Straka, to elements such as letters detailing their relationship with each other.
- Footnote Fever:
- F. X. Caldeira gratuitously uses footnotes not only to offer additional comments about Straka's life and his other works, but also to communicate through coded messages with Straka himself.
- On an almost meta level: when Eric & Jen annotate the book for the first time (the grey, black and blue handwriting) they put footnotes in it; then they go through the book a 2nd time (the green and orange writing) annotating on the original story again but also annotating on their own prior notes; then they annotate for a 3rd round (the red and purple writing), this time annotating on the story for the 3rd time plus on their original annotations plus on their annotations-on-their-annotations...
- Gecko Ending: In-Universe: As stated in the foreward, the ending of the final chapter is rewritten by Caldeira after Straka Died During Production. Several alternative endings, each purporting to be the real ending to the book, later emerge online. See Multiple Endings for more details.
- Hidden in Plain Sight: F. X. Caldeira inserts a few coded messages to Straka this way in an attempt to communicate with him. Hidden in the book's chapter titles and footnotes (additions by Caldeira) are the messages and the ciphers to be used to decode them. Some have been solved by Eric and Jen, while others have been cracked by readers.
- Left Hanging: The last chronologically known piece of marginalia in the book is written with a tone of ambiguity, leading to some speculation from readers as to the fate of Eric and Jen.
- Multiple Endings: Five alternate endings can be found online, each purporting to be the book's actual ending, lending credence to a comment by Eric in the foreward that a few versions of the ending exists, some of which are "obvious hoaxes". It remains unknown as to which ending, if any, is indeed the real one.
- Office Romance: There are hints that Professor Moody and his teaching assistant Ilsa are more than just colleagues.
- Plot Threads: The book has three of them.
- The book's main narrative, Ship of Theseus, tells of S.'s journey to discover his identity and becoming embroiled in a conspiracy.
- The forward and footnotes form another story unto themselves, offering commentary from F. X. Caldeira on Straka's personal life and other works, as well as Caldeira's interactions with Straka, including her attempts to communicate her Unrequited Love to him.
- The marginalia and feelies detail the interactions between Eric and Jen concerning the book and chart the course of their relationship becoming more interpersonal and eventually, romantic.
- Rewatch Bonus: Given its format, the book practically demands that readers read it multiple times, as it would be incredibly difficult to catch everything in one read-through. This is especially the case for the footnotes, which seem innocuous at first, but are actually hidden ciphers, and the marginalia, which are scattered throughout the book with different colors representing different time periods and comments in a given time period not necessarily being written in chronological order as they are encountered in the book. The Feelies also further complicate a smooth reading experience. A few strategies have emerged on how to approach the book, almost all of which mandate this trope. Doug Dorst has even stated that it is up to readers to decide how they themselves want to approach the book.
- Samus Is a Girl: In the Ship of Theseus inner story, S. finds out one of the sailors is a woman. He first assumed they all were men and it takes a really close look at the sailor for S. to realise it is a woman, mostly because the sailors all wear the same baggy clothing and the woman does not seem to have a "feminine-looking" face in the first place.
- Snark-to-Snark Combat: Conversations between Eric and Jen are brimming with snark:Jen: [...] Loved all the mystery—the book, Straka, all of it. I really needed an escape, I think.
Eric: Dear Undergrad Lit Major: If you thought it was an "escape" then you weren't reading closely enough. Want to give it another shot?
Jen: Dear Arrogant. I made some notes in the margins so you can see how closely I read. But what do I know? I'm just an undergrad.
Eric: I can't believe you wrote all over my book.
Jen: I know. It was so presumptuous of me.
- Year Outside, Hour Inside: Whenever S. is on the ship for what him feels like weeks, on land / outside of the ship years pass. One time when he gets on land he notices he has visibly balded, and aged for years, while on the ship for what for what for him felt like much shorter. This could be due to either the ship being a supernatural place (which is the Trope in the more strict sense), or to the psychological effects on S. of being on the ship. Remember he suffered memory loss from the beginning of the book on, he wasn't on the ship by will (initially), and none of the ship's other crew mention the time distortion, so possibly S. experiences this because of brain damage or a psychological protection mechanism.