The House in the Cerulean Sea

Linus Baker is a lonely case worker for the Department in Charge of Magical Youth ("DICOMY"), a governmental organization which manages orphaned magical beings who are minors. His job consists of visiting orphanages to check up on them and then writing up a report. One day, he's called in by the organization's Extremely Upper Management ("EUM") to serve on a month-long classified assignment, reporting directly to one of the four members of EUM, Mr. Charles Werner.

Linus's assignment is to assess a special orphanage on the island of Marsyas. The master of the orphanage is a man named Arthur Parnassus. There are six children living in the orphanage there, one of whom is called "Lucy" (short for Lucifer), who is the Antichrist.

All the children at Marsyas are unique. Theodore is one of the few wveryns in existence. Talia is a female gnome, a rarity. Phee is a particularly powerful forest sprite. Chauncey is an amorphous blog with tentacles, basically a monster. And Sal is a shapeshifter who can become a small Pomeranian, with the special ability of being able to give others shapeshifting abilities by biting them. He has been in many orphanages and was abused previously.

The children view Arthur as a father figure. There's also Zoe Chapelwhite, an undocumented, adult island sprite who has lived on the island since before the orphanage. She helps to take care of the children in an unofficial capacity. Linus is scared of the children at first, but soon sees that they act much like other kids. Arthur tells Linus that people see the kids as being threats, but actually the kids can be anything they choose to be. Meanwhile, the kids are scared that Linus will take away their home, since he will be making a recommendation whether to shut down the orphanage or not.

In previous assignments, Linus had prided himself on being detached and viewing the children's fates as outside the scope of his responsibility, but on Marsyas, Linus finds his objectivity slipping away. He also starts to develop romantic feelings toward Arthur, which are reciprocated. As Linus sends back reports to Extremely Upper Management, they are dismayed when they see how sympathetic Linus has become towards Arthur and the orphanage. Mr. Werner reveals to Linus that Arthur is actually a very rare magical being as well, a Phoenix. He gives Linus a key to a burned-out cellar on the island to show Linus how potentially dangerous Arthur can be.

When Linus goes to investigate, Arthur tells Linus that he grew up in a DICOMY orphanage and was abused. When he tried to ask the DICOMY for help, the master of the orphanage intercepted the letter and locked Arthur in the cellar. Arthur burned out cellar trying unsuccessfully to get out. He was eventually released when the DICOMY came to investigate months later. As an adult, Arthur requested to be put in charge of the orphanage because he wanted to turn it into a place where kids could truly get help. The required that he not tell anyone about being a Phoenix.

The people in the village of Marsyas fear the kids, but Linus encourages Arthur to take the kids into the village for the first time. Helen, the town mayor, is sympathetic to them and encourages the villagers to look past their prejudices.

When Linus's time on the island concludes, Arthur asks Linus to stay with him and the kids, but Linus declines. He goes back to the office and makes a recommendation to allow the orphanage to stay open. He also accuses the DICOMY of running discriminatory orphanages by segregating out the magical beings.

As soon as Linus's recommendation to keep the orphanage open is accepted, he know it's where he wants to be. He immediately quits his job and heads back. When they reunite, Arthur and Linus finally kiss. Later, Linus submits an anonymous whistleblower report about the DICOMY's discriminatory practices which results in the EUM all stepping down and being replaced. He also tells his story to a reporter who plans to publish an expose. Soon, Helen brings David, an undocumented yeti boy who needs a home, to the island. Arthur and Linus intend to formally adopt all the children, including David. The book closes with Arthur and Linus about to be married.

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