Emily urges her family to hurry up as they get ready for a fancy event at Hollister’s bookstore. Emily wears her Book Scavenger pin and a fancy dress that represents a break from her usual, casual style. Emily’s best friend James lives upstairs, and their two families begin their walk through the hills of San Francisco toward the bookstore. Emily remembers the dark sky and bright stars from when she lived in New Mexico. Here in San Francisco, the city lights muddle the view of the stars.

Emily feels nervous and excited for the event, where she, James, and her brother Matthew will be honored for having found a previously unknown Edgar Allan Poe manuscript several months prior. Most adults at the store are dressed in fancy clothes, but a few wear Poe costumes. Emily notices that nearly everybody wears a Book Scavenger pin. Book Scavenger is a book-hunting game where people hide used books in public and post clues on a website.

Emily looks for Mr. Griswold, the creator of Book Scavenger, and Hollister, the bookstore owner, but she first notices a pair of intimidating journalists. When Hollister comes over to greet Emily, the room falls silent. Emily feels increasingly terrified at the prospect of having to speak in front of the crowd. Hollister reveals that Mr. Griswold will not be attending the event tonight. Hollister and Mr. Griswold used to be best friends, but they had a falling out.

Jack, Mr. Griswold’s assistant, steps up to be the MC and introduce the kids. Jack surprises the room by lighting a screen with a video of Mr. Griswold.

In the video, Mr. Griswold assures everyone that he is recovering well from a recent incident in which he was attacked in a BART station. Mr. Griswold proudly recounts how Emily, James, and Matthew rescued the Poe manuscript, and Emily feels relieved that she won’t have to give a speech. One of the costumed people asks Emily and her friends to sign his book, making her feel like a celebrity. A classmate of theirs named Nisha asks them to sign her book in code. Emily and James use the cipher they made up together. Emily takes a break and checks on Herb, a bookmark bearing the image of legendary San Francisco journalist Herb Caen that she and James like to hide around the store. Emily is surprised to see her teacher, Mr. Quisling, in one of the aisles. She sees him reach into an unattended, floral-printed purse and steal something small and thin. Emily immediately reports what she saw to James. Before Emily and James can go interrogate Mr. Quisling, they are ambushed by a reporter. A fire engine roars by the bookstore, and the reporter receives a notification that a fire has broken out in Washington Square. Emily sees Mr. Quisling drop the stolen piece of paper, and James sneakily picks it up. Mr. Quisling introduces them to another Book Scavenger player named Harry Sloan, who compliments Mr. Quisling on winning a past book puzzle event. Harry pitches himself as a potential substitute teacher at school, but Mr. Quisling does not appear interested. Emily and James scrutinize the stolen paper and discover a clue in code.

That night, Emily and James exchange messages in their secret code through their window pulley system. James cracked the clue already and recognized it as a keyword cipher with the word “Niantic” as the key. The clue refers to an “unbreakable code.” James learns that the Niantic is a ship buried under San Francisco dating back to the Gold Rush. A piece of the ship is displayed at a museum. Emily and James plan to go investigate the display.

The Phoenix sits in a café watching news dispatches about the fire he started in Washington Square. Nobody has put together the pattern of fires.

Emily and James head to the Maritime Museum. Emily notices a massive ship moored to the end of the Hyde Street Pier for the first time. Emily finds the copper remnant of the Niantic and learns about its history. During the Gold Rush, Americans from the East Coast sailed all the way around South America to get to the West Coast, and ships brought gold seekers from other countries. An older docent shows them how much of downtown San Francisco used to be water just 150 years ago. Gold seekers were so eager to get up to mining country that they would abandon ships in the cove. Ships were broken down for materials, converted into shops and buildings, or buried. James asks the docent if she knows anything about an unbreakable code, and she refuses to discuss it with them, referring to the code as “cursed.”

The docent reveals that the code causes fires, including the one that destroyed the Niantic. Emily notices a picture from an excavation where volunteers dug up the Niantic. One of the young volunteers is a young Mr. Quisling standing with a woman later identified as Miranda Oleanda. Emily thinks the woman must be Mr. Quisling’s girlfriend. They consider asking Mr. Quisling about the unbreakable code but think better of it. They meet up with Matthew and pass the burned area in Washington Square.

Emily, James, and Matthew head to Bayside Press to work on the teen advisory committee they have been recruited to start for the Book Scavenger community. Jack warns the kids that Mr. Griswold is still a little rattled from his accident. Mr. Griswold apologizes for his frail, disheveled appearance and his excitable service dogs. He shows them the camera surveillance system he has set up to look at all parts of the office, revealing how much the attack has affected him. Emily and James excitedly pitch a big puzzle event in Golden Gate Park, but Mr. Griswold rejects the idea. Emily and James bring up some of the details they’ve learned about the unbreakable code. Jack knows it as a cipher associated with Mark Twain and suggests that the kids can find it at the library.

Emily, James, and Matthew debate their new information. Jack didn’t appear to know about the fire curse, and the docent hadn’t mentioned Mark Twain. Emily wishes to wander the massive library but decides to stay focused on the code. She is both impressed and intimidated by Regina Linden, the elderly librarian, who has colorful hair and tattoos. Ms. Linden identifies herself as a fellow treasure-hunter and brings them to a reading room to look at the code. Ms. Linden tells them about Tom Sawyer—not the fictional character, but the firefighter in San Francisco in the late 1800s who helped organize the first fire companies in the city. Apparently, Tom Sawyer and Mark Twain knew each other and were together when Mark Twain won the unbreakable code while gambling. He accepted the code as his winnings because legend has it that the code leads to a stash of gold buried beneath San Francisco. Mark Twain initially discounted the story about the fire curse until a fire started in his hotel room. He passed the code to Tom Sawyer, who displayed it in his bar for anyone to solve. Eventually, the bar burned down, but the code survived. Ms. Linden shows them the singed piece of vellum.

Emily scrutinizes the code, a collection of nonsensical letters. She finds the penmanship to be surprisingly juvenile. Emily gently traces the code into her notebook. Ms. Linden notes that nobody has looked at the code recently but says that perhaps she will start working on it now as well.

James’s family, the Lees, host Emily’s family for hot pot on New Year’s Eve. While the adults play mah-jongg upstairs, Emily, James, and Matthew play board games under a sheet they have converted into a fort. The kids think about how they want to live for the next year and agree that they want to spend time on Book Scavenger.

The next day, Emily overhears her parents talking about a client who has gone bankrupt. Money is tight now for Emily’s parents. Emily feels guilty that she made her parents promise to stay in San Francisco, an expensive city. Emily, James, and Matthew follow a Book Scavenger clue alluding to stones and music. Emily feels distracted by her parents’ money woes and plans to find a job.

As they pursue the clue, James takes Emily and Matthew on a detour to pick up It’s-Its, a local ice cream sandwich cookie. Emily quietly hesitates to spend money after hearing her parents’ conversation, but James offers to treat her. James leads them down the marina to the Wave Organ, an art installation where the lapping waves create music by interacting with giant concrete tubes. James notes that the stones used in the construction came from an old cemetery that was demolished. Emily looks in all the crevices until she finds a book called The Fourteenth Goldfish hidden beneath a brick. They celebrate by finally eating their It’s-Its. Across the bay, Emily notices Alcatraz and a smaller island beside it. James identifies it as Angel Island, a place where immigrants used to stop on their way into the country. James points out another island called Treasure Island, which reminds Emily of the unbreakable code. They consider what they would buy if they found buried gold. Matthew would buy a fancy guitar. James would buy a new computer. Emily decides she would buy night-vision goggles so she could do more book hunting.