The first book in The Drowning Empire trilogy is set in the Phoenix Empire, an archipelago of islands in an ocean called the Endless Sea. The Empire is ruled by Emperor Shiyen Sukai, whose family seized power centuries ago by defeating the Alanga, ancient magic-wielders who had ruled the islands. Shiyen governs through bone shard magic: During mandatory Tithing Festivals, a shard of bone is chiseled from every eight-year-old citizen's skull. These shards, inscribed with commands and placed inside animal-hybrid constructs, animate them as soldiers, spies, and bureaucrats, but the magic slowly drains the life of each shard's original owner.
The novel follows five points of view. On Imperial Island, Lin presents herself as the Emperor's daughter and heir. She has no memories from before a mysterious illness five years earlier, and her father refuses to teach her bone shard magic until she becomes "a whole person." Competing against her for the throne is Bayan, the Emperor's foster-son, who has recovered more memories and already studies the magic. Frustrated, Lin steals keys from her father's chain at night and commissions copies from Numeen, an Imperial City blacksmith who helps in exchange for Lin's promise to locate his bone shard. Through the palace's locked doors, she discovers the bone shard storeroom, books on the command language used to program constructs, and a green-covered journal hidden in the library. Written in handwriting nearly identical to her own, the journal describes a young woman's daily life. Lin assumes it records her forgotten past and uses its details to answer her father's questions, earning his trust.
Lin teaches herself bone shard magic, captures a spy construct, rewrites its commands to make it obey her, and names it Hao. She then undertakes a more dangerous project: rewriting the commands of Shiyen's four most powerful constructs. She succeeds with Mauga, the Construct of Bureaucracy, and Uphilia, the Construct of Trade. While searching Uphilia's nest, she finds a birth record listing "Lin Sukai, 1522–1525," suggesting Lin died at three years old.
Across the Empire, Jovis, a smuggler and former Imperial navigator, has spent seven years searching for his wife, Emahla, who vanished one morning with nineteen silver coins left on her bedspread. On Deerhead Island, he learns from Danila, the foster mother of another vanished young woman, that a fisherman saw a dark-hulled boat with blue sails heading east. When earthquakes strike and the island begins sinking, Jovis rescues Danila's nephew Alon from the Tithing Festival, dumps his cargo of witstone, a valuable magical fuel, to lighten his boat, and barely escapes. He scoops a small brown creature from the waves; Alon names it Mephi after a legendary sea serpent.
As Jovis pursues the blue-sailed boat, Mephi grows rapidly and begins to speak. A bond forms between them that grants Jovis supernatural strength, the ability to shake the ground, and accelerated healing, though the power vanishes whenever Mephi is ill. Desperate parents pay Jovis to rescue their children from Tithing Festivals, and a folk song about his exploits spreads across the Empire.
On Nephilanu Island, Phalue, the governor's daughter, struggles with her lover Ranami, a former gutter orphan turned bookseller who repeatedly refuses Phalue's marriage proposals. Ranami refuses to become "a governor's wife" while Phalue's father ships all the island's caro nuts to wealthy markets, denying farmers the nut oil that cures bog cough, a disease killing their children. Ranami introduces Phalue to Gio, the one-eyed leader of the Shardless Few, a rebel movement seeking to abolish the Tithing Festivals and replace the Emperor with a representative Council. Phalue reluctantly helps steal caro nuts for the farmers, and visiting the communal barn where farmers live forces her to confront the injustice her privilege has concealed. When her father imprisons her for the theft, a palace guard reveals that commoners who steal are routinely executed.
On Maila, a remote island at the Empire's edge, a woman called Sand lives with roughly two hundred others—all transported there by the blue-sailed boat that Jovis pursues—in a fog of compulsion, performing daily tasks without question. After falling from a mango tree and injuring her arm, Sand's mind clears. She discovers that none of them can remember their pasts, and through persistent questioning she draws a few others out of the fog. They all recall arriving on a boat with blue sails. Sand also experiences vivid memories that are not her own: a palace with painted beams and a handsome man in silk robes. She organizes a plan to seize the boat when it returns.
Lin's plans unravel when her attempt to rewrite Ilith, the Construct of Spies, fails. Ilith's commands prove far more complex, and the construct begins to deteriorate, revealing that the Emperor has known about Lin's stolen keys, her blacksmith, and her entire conspiracy. Lin races to warn Numeen, but Tirang, the Construct of War, arrives first and kills Numeen and his entire family. The Emperor confronts Lin, praises her ingenuity, and reveals that Bayan is a construct he built. Lin is knocked unconscious.
She wakes locked in her room. Reviewing the journal, she realizes its entries describe experiences inconsistent with growing up on Imperial Island. The Emperor visits and reveals the full truth: He grew Lin in caves beneath the palace from stolen fragments of other people, intending her as a vessel for the memories of his dead wife, Nisong Sukai. Bayan was built as a copy of the Emperor, intended to eventually house Shiyen's consciousness. A hidden note inside the journal's back cover reads "Nisong will rise," confirming the journal belonged to Nisong. Devastated but resolute, Lin escapes by commanding her spy constructs to unbar the shutters. She convinces Bayan they are both constructs by pushing her hand into his chest, demonstrating that his body responds to bone shard magic as a construct's would.
Together they confront the Emperor in the dining hall with Mauga, Uphilia, and Bing Tai, the Emperor's oldest construct. The Emperor summons waves of war constructs, and Bayan is killed when Bing Tai seizes him by the throat. Drawing on a flash of Nisong's memory, Lin realizes that Bing Tai was originally created by Nisong and commanded to obey her first. Lin claims this authority, and Bing Tai turns and kills the Emperor.
Lin descends into a hidden laboratory and discovers the Emperor's memory machine, a device designed to implant and transfer memories between bodies. She also finds a large, sickly creature connected to the machine by tubes, resembling a larger version of Mephi with spiraling horns. Lin frees the creature and names it Thrana after Numeen's murdered daughter. As she leaves the cavern, she notices that the eyes of the Alanga figures in the palace's entrance mural have opened.
Jovis, having accepted that Emahla is almost certainly dead, travels to Imperial. He fights and kills a four-armed construct on the palace steps that confirms Emahla died years ago. During the fight, Jovis discovers he can manipulate water. Inside the palace, he encounters Lin, who identifies herself as Emperor and offers him the position of Captain of the Imperial Guard. Jovis accepts, though he has secretly promised the Shardless Few he will send them intelligence.
On Nephilanu, Phalue frees herself from prison during the Shardless coup, deposes her father, and claims the governorship. She proposes to Ranami one final time, and Ranami accepts. On Maila, Sand finds a bone shard near where she fell and realizes she and all the island's inhabitants are constructs, their compulsion governed by shards embedded in their bodies. Her group captures the blue-sailed boat. When the Emperor dies, a shockwave lifts the fog permanently. Sand reclaims the name Nisong, drawn from her memories of life as the Emperor's wife, and declares they are building an army. Lin pledges to end the Tithing Festivals and remake the Empire.