Linus Baker is a case worker who has been assigned by the Department in Charge of Magical Youth (“DICOMY”) to investigate an incident at an orphanage. Daisy, 11, used her powers to throw a chair at another kid, Marcus. Linus suggests that perhaps some type of “extreme emotion state” triggered her powers.
Among the kids there, there’s also a witch, a siren and a selkie. After the getting the information he needs to file his report, Linus leaves.
When Linus returns to his office, Bedelia Jenkins, his supervisor, approaches him along with her assistant, Gunther, to inform him that Extremely Upper Management (“EUM”) has requested that Linus attend a meeting tomorrow, something that’s never happened before. Neither he nor Ms. Jenkins knows why. Gunther also gives Linus a “demerit” for having a stain on his shirt.
At the end of the day, Linus returns to his small and modest home at 86 Hermes Way. His neighbor, Edith Klapper, is an older (“ancient”) woman, and she complains to him that his cat Calliope has been chasing squirrels in her yard. Linus found Calliope 10 years ago when she was a kitten, walked into his house and refused to leave. Mrs. Klapper also comments on how he never seems to have plans, and offers to set him up with her grandson, which Linus declines.
That night, instead of thinking about how he’s 40, lonely and could afford to lose a few pounds, Linus reads the Rules and Regulations for his workplace to prep for tomorrow’s meeting.
The next day (on Wednesday), he arrives two hours early for work. Then, at 8:45 AM, he heads up to the 5th Floor, where he’s never been before, for the 9:00 AM meeting. He announces himself to the receptionist (who he nicknames Ms. Bubblegum), and soon is told that all four members of Extremely Upper Management (three men, one woman) are waiting to meet with him. Of the three men, one has jowls, one has spectacles and one is handsome-looking.
At the meeting, they make note of Linus’s 17-year tenure with DICOMY and his thorough work. They complement his emotional detachment when doing his work, but they also ask questions to assess whether he cares about the children, which he assures them he does. Finally, they talk about discretion about how what they’re about to tell is classified level four, which is the highest classification level.
There is an orphanage that concerns them. There are six children there, and they are “problematic”. The master in charge of the orphanage is named Arthur Parnassus, and Linus’s task is to ensure that Mr. Parnassus “continues to be capable of managing them” or if the orphanage should be shut down. The orphanage is located on the island and Linus is to spend one month there, starting tomorrow.
For this assignment, he will be reporting directly to one of them, Mr. Charles Werner (the handsome one), but all four of them will be involved. They also stress the need for extreme detail when report his findings back to them.
The next morning (on Thursday), Linus boards a train for Marsyas with Calliope in a crate. The island he’s headed to is a ferry-ride away from Marsyas. Riding on the train, he sees the cerulean waters of the ocean for the first time, marveling at its beauty and expansiveness.
At the Marsyas train station, he waits to be picked up. He has with him files on all six children and Mr. Parnassus. He also has a letter outlining his assignment, along with a warning that he should lock all doors and windows at night for protection. As he browses the first child’s file, he sees a photo of a six-year-old boy, named Lucy. Then he realizes it’s short for Lucifer and the boy is the Anti-Christ. Linus faints.
The woman sent to fetch him eventually wakes him up, identifying herself as Ms. Zoe Chapelwhite, the Caretaker of Marsyas Island. As Ms. Chapelwhite drives them to the ferry, she explains that there’s nothing wrong with the children at the orphanage and that they’re not what he thinks. She also reminds him that his job is to protect them.
While they talk, it dawns on Linus that Ms. Chapelwhite is an island sprite (she’s barefoot, takes care of the island, etc.) which she reluctantly admits to. She’s also unapologetically unregistered (magical beings are supposed to be registered). Ms. Chapelwhite notes that the people of the village of Marsyas are not accepting of magical beings of any kind. In the village, Ms. Chapelwhite takes Linus to Merle the Ferryman , who then ferries him to the island and brusquely tells him to get out of the boat as soon as they arrive.
Alone now on Marsyas Island, Linus drives along the single road through an old forest until he finally reaches a house situated on a cliff that overlooks the ocean.
As soon as he opens Calliope’s crate, she runs out. He follows his cat, which leads him into a lush garden. He then inadvertently meets Talia, a gnome. Talia is 263 years old, but she’s considered a child because gnomes reach maturity at 500.
When he explains about his cat, Talia calls for Theodore to help find Calliope. Theodore is a wyvern, and he swoops in as requested. Talia explains that Theodore is willing to help, but Linus must pay him a coin (for Theodore’s hoard) in exchange. Linus only has a button, but Theodore is delighted with it. Talia then explains that she has tricked Linus, and Theodore won’t help him find Calliope.
Before Linus can protest more, Phee appears. She looks like a young girl, though she is a forest sprite. Linus recalls that young sprites are more dangerous because they are not in control of their magic. When Linus inquires about Arthur Parnassus’s whereabouts, Talia says from 5 PM to 7 PM the kids do what they want while Arthur works with Lucy.
Phee tells them that the cat’s not in the woods, so Talia suggests they find Sal, who turns out to have Calliope. Sal has the appearance of a large black boy, but then he suddenly shapeshifts into a fluffy, 5-pound Pomeranian. Talia explains that it happened because Linus scared Sal. Sal then barks and runs away.
Inside the house, Linus meets Chauncey, an amorphous tentacled green blob with red lips and black teeth. Chauncey seems to have some degree of mind control, though he aspires to be a bellhop. Before Linus can fully react, Lucy introduces himself as “evil incarnate”.
In Lucy’s presence, the sky suddenly falls to darkness, which scares Linus. But then Arthur tells him to cut it out and things return to normal. Arthur introduces himself, while Linus struggles to regain his authoritative footing after being thrown off-kilter by the children.
There’s a little time before dinner will be served (at 7:30 PM), so Linus has a little time to settle in his bedroom in the guest house. His window overlooks the ocean. He finally has a chance to really look over the files, and he chides himself for not doing so before arrival.
Just before dinner, Linus makes his way to the kitchen and finds Ms. Chapelwhite cooking dinner with Lucy assisting her as they bounce around to music (Bobby Darin). As they sit for dinner, the kids direct various ominous-sounding statements and threats toward Linus, though Arthur scolds them for doing so. Over dinner, Talia is inquisitive about Linus, to his discomfort, and asks about why he only eats salad (trying to diet) and about his marital status.
Finally, just before dessert is served, the kids ask Linus whether he’s going to “take our home away from us”, but Linus isn’t given a chance to answer.
After dinner, Arthur shows Linus the locations of the children’s rooms. Lucy shares a room with Arthur, a converted walk-in closet, because of the nightmares he otherwise used to get.
In Arthur’s office, he and Linus sit down to talk. Arthur is somewhat critical of Linus’s line of work, pointing out that the term “orphanage” is a misnomer, since magical kids never get adopted. The Department in Charge of Registration deals with magical families, and the DICOMY deals with magical orphans. Arthur sees how those orphans get shuttled off into orphanages and schools and are essentially taken out of circulation.
Arthur criticizes Linus’s attitude about his job as well. Linus focuses on his job and doing it well, but he takes the stance that what the rest of the DICOMY does with the kids and the orphanages after Linus writes up his report is someone else’s responsibility and doesn’t think about it. He claims to care about these kids, but is uncurious about their outcomes.
When Linus refers to Lucy as the “antichrist”, Arthur rebukes him sharply, explaining that using that word isn’t permitted here. With regards to Chauncey, no one really knows what exactly he is. Chauncey spent his whole life prior to coming here believing that he was meant to be a monster, scaring people by hiding under beds and whatnot. It wasn’t until recently that he was told that he could choose something else, and he chose to be a bellhop.
Arthur also says that Sal is scared of Linus because he is a case worker. Sal has been in 12 orphanages in the past and he has a general understanding of the case workers’ role is in that. While there are plenty of other shapeshifters in other DICOMY orphanages, Sal is unique in that he can pass along the shapeshifting ability by biting someone.
Talia is here because she’s unique in that all other gnomes are male. Also, Phee is here because she is uniquely powerful and needs to learn to control her powers responsibly, which Ms. Chapelwhite assists with. Theodore is a young wyvern and there aren’t very many wyverns left in general.
The next morning (on Friday), Linus wakes to find Chauncey hiding under his bed. Chauncey says he’s just there to tell him to come down for breakfast. Linus also prepares his first report to be sent to the DICOMY, where he comments on the “woefully inadequate” information he was given prior to beginning the assigned.
This morning, Linus watches as the kids perform or tell stories in front of the class. After lunch, Ms. Chapelwhite demands that Linus come with her, which results in a strenuous walk through the woods. They reach the beach on the other side, and there is a poorly-made raft with a message: “LEAVE. WE DON’T WANT YOUR KIND HERE”. Ms. Chapelwhite explains she’d gotten a number of these messages. She doesn’t want Arthur to know, but she thinks Linus should include it on his report.
Linus is upset at the idea that the village people are harassing the people on the island. He suggests to Ms. Chapelwhite that they send a message back. He writes “No, Thank You” on the raft, and Ms. Chapelwhite harnesses her powers to have the wind to carry the raft back in the other direction.
While Linus finishes up his first report, Linus is invited by Arthur to sit in on one of the sessions with Lucy, so he can understand what goes on. Linus knows that EUM is like more interested in Lucy than the rest of the kids, so he accepts despite his deep fear of Lucy. Linus is also curious to know more about Arthur, but tells himself it’s for the sake of being thorough on his report.
Linus has never been religious, despite his mother wanting otherwise, especially since he realized he was gay as a kid. However, now he finds himself wishing he had a bible or crucifix with him to protect himself. Linus goes to join Lucy and Arthur. Lucy acts like a normal kid in some ways, but he also has a fixation on death. Arthur tries to steer him towards more humane and normal thoughts.
After the session, Linus and Arthur talk, and Arthur explains that like the other kids, Lucy just need hope and less prejudice. Linus points out that the children being isolated on the island doesn’t do much to fight prejudice, but Arthur insists it’s for their own good.
Arthur also reveals that there was a former caseworker who had come to their island before. That caseworker was planning on staying with them at the island, but then he got promoted and promoted again into EUM and his attitude changed. Linus realizes the caseworker was Mr. Werner (the handsome one), and it’s implied that he and Arthur had a romantic relationship.
The next morning (on Saturday), Linus takes the ferry to the village to get to the post office and drop off his report. He has an unpleasant encounter with the postal worker who says bigoted things about the kids and people on the island.
That day is also the second Saturday of the month, which is when Zoe and Arthur traditionally take the kids on an adventure. Zoe drops off a safari-type outfit for Linus which he reluctantly dons, feeling ridiculous. With them all dressed up like a troupe of explorers, they all head off for the woods.
When Linus starts talking about possible violations of the Rules and Regulations, Arthur dismisses his concerns. Arthur points out that it’s inherently misguided how the rules were written by humans and that no magical beings had a say regarding rules that are supposedly aimed at the well-being of magical creatures. When Linus says that the rules are meant to help them assimilate, Arthur question why they need to assimilate at all.
As they go deeper into the forest, Zoe and Arthur put on a game that leads the kids to Zoe’s house in the woods. Sprites are notoriously private and protective of their homes, so Linus know what a big deal it is for Zoe to allow the kids into her home. They happily have lunch there, and Linus listens to Phee and Zoe talk about their sprite-ly powers. When Linus talks about missing his sunflowers at home, Phee grows a small bush daisy, a yellow flower, for him, and he is delighted.
In Linus’s second report, he writes about how Zoe helps to care for the kids. He says that so far, Lucy seems like a mischievous boy who mostly says or does things for “shock value” without real malicious intent. He also says they’ve bonded over their shared love of similar music, but Linus know he needs to keep an eye on him. He also writes that he’s concerned about the isolation of the island and how the village inhabitants (who are paid to keep quiet about the island) are hostile to the islanders. Linus worries that it will be difficult to assimilate the kids with such isolation.
On Tuesday, Calliope fancies a chase and runs off with Linus’s tie. Linus goes after her. They end up in the garden where he discovers a cellar door with a rusted padlock.
For his investigation, Linus has been talking to all of the kids and asking if they are happy there, which is standard in his visits to orphanages here. But here, the kids do seem to be genuinely happy. Linus also recognizes that he’s developing highly unprofessional feelings for Arthur, which is not acceptable since Arthur is one of the subjects of his investigation.
Around the halfway point of Linus’s month-long trip, Sal offers to let Linus see his room. In the closet, there’s a desk with an Underwood typewriter, and Sal explains that he likes to write because it helps him to “find order”. He started writing after came to Marsyas. Linus suggests putting the desk near the window instead, and he helps Sal move it out of the closet. Sal talks about how he’s happy here and he never wants to have to move again, but he’s worried that Linus will make them move. Sal brings up the incident when he bit someone who hit him and she became a shapeshifter, too, and he promises it will never happen again.
That night, Arthur stops by with a gift, a vintage Zenith record player, which he says was Lucy’s idea. Linus is very touched and lobes the gift. As the two men chat, Linus brings up his idea of taking the kids on an outing away from the island. Arthur is uncertain, but agrees to consider the plan.
At the post office a few days later, Arthur receives a letter from Mr. Werner. It expresses concern about Zoe’s presence with the kids, and it requests greater detail about Arthur.
Afterwards, Zoe tells him that as it is the third Saturday of the month, they will be picnicking in the garden for lunch and that it’s Chauncey’s turn to choose the menu.
In Linus’s third report, he updates EUM on his thoughts about the isolation of the kids. He also includes a reminder that the Rules and Regulations are guidelines, rather than law and that they haven’t been updated since they were written decades ago. Linus says that he thinks Zoe helps Phee to have much more control over her powers. He also mentions that there’s documentation that Sal was physically abused prior to his arrival at Marsyas, and Linus wonders why that wasn’t in his file. As he talks about how all the kids have grown and improved, he attributes it all to Arthur’s stewardship of the orphanage.
One night, Linus awakes to find his bed hovering in the air. Zoe soon comes in, looking concerned, saying that Lucy is having a nightmare. Downstairs, the kids are gathered and they say that occasionally this happens and it causes their beds or the whole house to shake. He realizes that they are trying to convince him that Lucy is not dangerous, since they are afraid of what he’s going to write in their report.
Linus goes to Lucy’s room to see Arthur holding him, trying to beckon him a distressed Lucy out of his nightmare. Finally, Lucy slumps over, awakened. Lucy is upset to see he has broken some of his favorite records. Linus offers to help fix them, and finally Arthur proses that they go to a record store in the village where they can replace them.
Afterwards, Arthur is concerned about what Linus’s report will say about this incident, but Linus tells him he understands and the two share a moment.
On ferry across to the village, Linus warns Lucy not to go around making foreboding pronouncements to scare people in the village. Chauncey is dressed in a trench coat as a disguise.
It’s now been three weeks since Linus first stepped foot in the village. As they get out of the van, the children are told to pair up. Lucy and Talia are to go with Linus. Sal and Theodore are with Arthur. Phee and Chauncey are with Zoe. Arthur has also given them allowances beforehand so they can buy things, and the plan is to meet up a little later at the ice cream parlor.
At the hardware store, Lucy gets excited about the gardening supplies and a spade in particular. A woman in the store looks scared when she recognizes that they are from the island, but Talia calms her fears as she launches into a discussion about her garden. When Talia wants to buy more things than her allowance will allow, Lucy offers to give up some of his allowance, but Linus rejects that idea and pays with a credit card instead.
At the record store, the attendants, J-Bone and Martin “Marty” Smythe, chat with Lucy and offers to help him to find some records. However, when they take Lucy into the back, Linus hears a loud noise. He breaks the door open to see Marty slumped over. Lucy said that Marty started yelling at him and trying to shove a crucifix in his face. J-Bone agrees that Marty deserved it and was out of line, and he lets Lucy have his records for free.
When an older woman yells at Talia for being a “freak”, Lucy asks if he should throw her against a wall like Marty, but Linus and J-Bone try to remind him that it’s only okay to get physical to defend yourself and others, and just because someone else acts poorly doesn’t mean you should as well. Talia is not upset by the incident, focusing on how another little girl wasn’t scared of her at all. She recalls how Arthur previously told her that “in order to change the minds of many, you have to first start with the minds of few.”
The kids all have a fun time, but at the ice cream parlor, the man there, Norman, refuses to serve them. When Norman yells, the kids get scared. Arthur gets angry, but Linus calms him down. Then, a woman walks in, who turns out to be the gardening lady from the hardware store. She’s actually the owner of the store as well as the mayor of Marsyas. The woman, Helen, demands that Norman serve the kids. Norman stalks out angrily, and Helen offers to do it instead.
Helen says that she used to serve ice cream when she was a teenager, and Arthur used to come in for ice cream as a kid. She also says that Marty is her nephew and she’ll talk to him about his behavior.
Afterwards, Linus heads to the post office where a letter from Mr. Werner is waiting. Mr. Werner expresses concern that Linus is being less objective about his observations than they had hoped. Furthermore, Mr. Werner suspects Linus is being charmed by Arthur and finally includes Arthur’s full file so that Linus can understand him better. He also encloses a key to the house’s cellar door “give you insight as to what Arthur Parnassus is truly capable of”.
Back at the house, Linus frets over the letter and finally opens the file on Arthur. What he reads shocks Linus, and he wonders if perhaps the DICOYM is lying to him. That night, he makes his way to the cellar door. He goes in to see it is covered in soot. There’s a partially burned desk and broken bed as well. There’s also tick marks from someone counting down the days on the walls.
Then, Linus hears that Arthur has followed him down there. Linus asks if it’s true that Arthur is a phoenix, and he says yes. He says he’s the only one he knows of. He says that when he was young, he couldn’t control it. The master of the orphanage then was cruel and abusive to them, so young Arthur wrote to the DICOMY for help, but the master intercepted it and locked him in the cellar. He tried to burn his way out, but it didn’t work. Six months later, he was finally released when the orphanage was shut down. The DICOMY later put him in charge of the orphanage when they reopened it out of some combination of guilt and wanting to keep him quiet about what had happened to him.
As Arthur talks, he lets his wings of fire burn freely so Linus can see them. Then, he folds the phoenix back into himself.
Arthur says this island was meant to be an isolated experiment for the DICOMY to get rid of problematic magical creatures, but Arthur and Zoe were determined to turn it into a place where kids who really needed help could get it. Arthur didn’t reveal what he was to the kids or Linus because he was told not to by the DICOMY.
Soon, Linus is saying his goodbyes as he prepares to depart the island. He wonders if he’s doing the right thing by leaving, but he reminds himself that this was always temporary. One afternoon on the Wednesday prior to Linus’s departure, Theodore gets his attention, indicating that he’s ready to show him his hoard, which is a big deal for Wyverns. In his collection of treasures, there are coins, rocks, buttons, and items that represent each of the people in the house (a photo of Arthur, a broken piece of a record, a dried flower, etc.). He then gives Arthur a button as a gift.
The next day, Zoe senses that the people from the village have gathered near the shore and are headed toward the island, and she can feel their anger. As Arthur prepares to go meet them, Linus volunteers to go as well, saying that a voice representing governmental authority may help. At first it seems like they will be unable to cross because the ferry is on the other side of the crossing, but Arthur tells Linus to trust him. Linus drives across the water and realizes that Zoe has created a road of salt for them to drive over.
On the other side, Merle is preventing people from crossing into the island. At first, Linus thanks him, but Merle makes clear that his issue was that they didn’t want to pay the crossing fee. Nearing the crowd, they see that Marty is wearing a neck brace and riling up the crowd, telling them about how he was injured by Lucy. But Helen says that Marty didn’t get that neck brace from a recent doctor’s visit, instead, she recognizes as one she needed after an accident a long time ago. She points out that her initials are even on it.
As the crowd argues against Linus, Arthur and Helen, someone throws a rock. It prompts Arthur to transform into his Phoenix form in order to protect them. When he folds the phoenix back into himself, the people are too shocked to keep raging. Arthur takes the opportunity to make a plea to the townspeople to be understanding of the kids on the island. And Helen reminds them that there will be legal consequences if anyone tries to get violent. Afterwards, Arthur and Linus head back to the island.
On Friday, the day prior to Linus’s departure, the children show up in the morning to invite him to an adventure. The group makes their way back into the jungle, pretending to be fighting off cannibals and snakes. They get to Zoe’s house once again, and they have a party.
That night, Lucy tells Linus that he doesn’t want him to leave them, but Linus responds that he has to leave because he has a job to do. After the kids go to sleep Linus walks downstairs to see Zoe and Arthur arguing. Then, Zoe leaves. Linus asks what it was about, and finally Arthur works up the nerve to ask Linus to stay with them. Linus responds with “you know I can’t”.
Early the next morning, Linus is picked up by Zoe, and they meets Merle at the dock to cross over. Zoe is clearly unhappy with Linus for leaving them. She takes him to the train station, and Linus boards the train.
It’s rainy and grey when Linus gets home. He sees that his sunflowers are gone, and Mrs. Klapper tells him that they died in his absence, so she had someone come pull them out.
He goes to sleep, and the next day he awakes to do his laundry. As the opens his suitcase, he sees that laying on top is a brown envelope. Inside is a photo of him and Arthur with all the kids, taken that first Saturday at Zoe’s house.
Back at work, no one says hi to him. He puts up the photo at his desk, but personal effects are against the rules, so Ms. Jenkins gives him 10 demerits when he refuses to remove it.
The next day, Linus has a meeting with EUM again. He brings his final report with him. At the meeting, EUM expresses dissatisfaction with him. His final report merely states his recommendation that the orphanage stay open and under the guidance of Arthur, without further explanation. They also get into an argument with Linus about whether Lucy is innately “immoral” given that he is the Antichrist. Linus argues that Lucy can be whatever he wants to be, but EUM argues that Lucy was simply born with “wickedness”. Linus then says that his real father is Arthur, not anyone else.
As the argument escalates, Linus accuses the DICOMY rules of being prejudicial by segregating off these magical beings. He also says that they should just call them “homes” and not “orphanages” since that’s what they are. Mr. Werner tells Linus that he has disappointed him, but Linus doesn’t care. Finally, they tell him they will consider his recommendation and dismiss him coldly.
As he exits, Ms. Bubblegum the receptionist comments on how loud he was in there, and Linus goes back to his office to work.
Three weeks later, Linus has been thinking about the kids he’s left behind in all the orphanages, and he starts smuggling out old reports that he and others have written up, with a plan of following up on them (something he never did before, since he didn’t considered it to be part of his responsibility what happened after he did his job of writing up his reports). It’s against the law, but he does it anyway.
One day, Ms. Bubblegum comes down to his desk. She introduces herself as Doreen, finally. She hands him a file. When she leaves, he opens it to find that EUM has approved his recommendation for the Marsyas orphanage to stay open.
With that, he grabs the photograph from his desk and goes home, packs his things and gets on a train headed for Marsyas. From the station, he walks to the village (noting to himself that he hadn’t entirely thought his plan through). He runs into Helen, who helps ensure that Merle will ferry him over.
When Linus gets to the house, Calliope runs into the garden. Linus goes after her and finds Talia there, who cries when she finds out he’s planning on staying. Soon, Linus announces his intention to stay to the other kids, who “talk it over” and happily agree. Arthur then asks him what exactly happened, and Linus tells him about the orphanage staying open and about the files he took. Finally, Arthur kisses him.
As time passes, Helen tries to convince the villagers that she can sell Marsyas as an inclusive vacation spot, for both humans and magical beings, to bring in more business. This business proposition helps to quiet the village, especially after they stop being paid hush money (to not say anything about the island) from the government.
Furthermore, an investigation into DICOMY as a result of an anonymous whistleblower declares that its schools are discriminatory, resulting in the resignation of all members of EUM. The new members of the board promise changes, though “overhauling decades of preconceptions would take time”.
A reporter later asks Linus if he was the rumored whistleblower. It results in him telling her his full story, which she intends to publish. It’s also implied that Arthur soon intends to testify to the government about his experiences as a ward of the DICOMY.
One day, Helen tells them she’s found an undocumented boy who needs a home. His name is David, he’s 11 and he’s a yeti. David prefers it cold, so Arthur thinks they can convert the cellar into a cold room.
Arthur and Linus intend to formally adopt all the children, including David. The book closes with Arthur and Linus about to be married.