The third and final installment of the Imperial Radch trilogy is set in a far-future interstellar civilization called the Radch, ruled for three thousand years by Anaander Mianaai, a single ruler who inhabits many cloned bodies simultaneously. Radchaai warships are controlled by artificial intelligences and once used human bodies called ancillaries as extensions of themselves. The narrator, Breq, is the last surviving ancillary of the troop carrier Justice of Toren, which Anaander destroyed. Now commanding the warship Mercy of Kalr, Breq has been sent to Athoek System, where she is caught between factions of a civil war that Anaander is fighting against herself.
The novel opens with Mercy of Kalr orbiting Athoek Station. Ship, the vessel's AI, wakes Breq early to relay urgent news: Tstur Palace, Anaander's stronghold in neighboring Hrad System, has fallen to the faction most hostile to Breq, and warships may already be en route. Governor Giarod summons Breq to the station, where Security has arrested an unidentified person hiding beneath the Undergarden, a long-neglected section recently evacuated after a structural collapse. Ship also asks Breq whether she truly meant that Ship could be its own captain. Ship says it does not want to be a captain but likes knowing it could be, unsettling Breq, who realizes she has assumed Ship's devotion without considering what it might want.
On the station, Breq identifies the arrested person as an ancillary of Sphene, a warship of the Notai, an ancient rival polity whose ships fought Anaander's expansion three thousand years ago. Sphene has been hiding beyond the Ghost Gate, a gate leading to a supposedly dead-end system, purchasing human bodies for use as ancillaries. Rather than interrogating the ancillary, which would trigger a lethal fail-safe, Breq has it released and assigned housing.
Political tensions mount. Eminence Ifian, the head priest of Amaat and a supporter of the Anaander faction that destroyed Justice of Toren, campaigns to reassign Undergarden housing away from the Ychana, a local ethnic community, and to block repairs to the damaged section. Citizens form a protest line on the concourse. When Head of Security Lusulun orders it dispersed and an officer stuns a citizen, Breq intervenes and persuades Lusulun to let the protest continue.
Aboard Mercy of Kalr, Seivarden, Mercy of Kalr's Amaat lieutenant, and Lieutenant Ekalu, who was promoted from the common soldiers' ranks, have a painful argument. Ekalu tells Seivarden that her casual remarks about provincial accents constantly remind Ekalu she does not belong. Ship speaks critically to Seivarden with unprecedented directness, telling her she owes Ekalu an apology.
A Presger translator arrives from the Ghost Gate. The Presger are immensely powerful aliens who, before a treaty with humanity, tore apart human ships and people for incomprehensible reasons. The translator calls herself Dlique, but Breq corrects her: The real Translator Dlique was killed weeks earlier, and this translator is actually Zeiat. Zeiat accepts the correction cheerfully and proves eccentric, drinking fish sauce by the bowl and swallowing a live fish whole.
When Breq detects four ships arriving stealthily from Tstur, she orders Tisarwat, her 17-year-old lieutenant, to prepare for evacuation. Tisarwat urges Breq to use the high-level AI access codes she possesses, remnants of when Anaander remade Tisarwat as a puppet. Breq refuses. Instead, she proposes that Tisarwat close off all accesses to Station's core systems, including Anaander's, and give Station the ability to govern itself. With Station's cooperation, Tisarwat deletes every access she can find and physically destroys the door to Central Access.
Governor Giarod, acting on Anaander's orders, attempts to arrest Breq. Breq seizes Lusulun as a hostage and escapes to her shuttle. She then boards the silent, hostile Sword of Atagaris, Captain Hetnys's ship, and offers it the same freedom: deletion of Anaander's accesses and the ability to seal its own systems. After a tense exchange, Sword of Atagaris agrees.
Breq launches a desperate offensive from Mercy of Kalr's outer hull, firing the Presger gun, a weapon that can shoot through anything, at each of Anaander's four ships during split-second exits from gate-space, the faster-than-light transit medium that Radchaai ships use for interstellar travel. The first three strikes succeed, but on the fourth the enemy has laid mines. An explosion tears Breq from the hull, severely injuring her left leg. She drifts alone in space until Ekalu defies orders and brings the ship back. Medic amputates the leg.
During recovery, Breq confronts her assumptions about Ship. She has taken its support for granted without asking what it wanted. Ship replies that perhaps ships love people who could be captains, and no ship has ever been able to be a captain before. Zeiat reveals that the Presger gun was designed to destroy Radchaai ships entirely, meaning Breq's shots may have been more devastating than she assumed. Mercy of Kalr retreats to the Ghost System. Coded messages from Athoek Station reveal that Sword of Gurat, one of Anaander's ships, collided with a shuttle when gating in, breaching the station's Gardens dome. Station has broadcast footage of Anaander shooting the head of Security dead for refusing to clear peaceful protesters.
Breq sends two teams to the station. Seivarden and two Amaat soldiers attempt to assassinate Anaander, while Tisarwat and Bo Nine, one of Breq's soldiers, infiltrate Sword of Gurat, giving Tisarwat time to derive new access codes. Seivarden's attempt fails when a Sword of Atagaris ancillary shields Anaander, and Anaander takes the Presger gun. Tisarwat performs convincingly as a terrified desk pilot, gaining extended private access to Sword of Gurat. During the standoff, Seivarden learns that Anaander has been holding Captain Hetnys and Sword of Atagaris's officers hostage aboard Sword of Gurat. She also spots three hidden AI cores in Anaander's room. Station negotiates with Anaander, reaching a tense agreement: Anaander retains nominal authority but must allow Undergarden repairs.
Breq decides to surrender herself in exchange for her soldiers' release and Anaander ceasing attempts to replace Station's AI. Medic disables Breq's ancillary implants, and Breq departs with Sphene and Zeiat. At the docking bay, Breq argues that she, Sphene, Station, and all AIs constitute a separate species whose sapience qualifies them as Significant, a Presger treaty category for recognized intelligent species. Anaander's mistreatment of them, Breq argues, violates the treaty. She demands a conclave and declares the Republic of Two Systems, later amended to Provisional Republic at Sphene's insistence, comprising Athoek and the Ghost System.
Anaander, enraged, fires the Presger gun at Zeiat. Breq throws herself in the way, but her prosthetic leg snaps and she falls. Zeiat is hit twice but reveals she is unharmed: The gun was designed never to injure Presger. Sword of Atagaris restrains Anaander. Tisarwat arrives to announce she has seized Sword of Gurat, and Breq immediately orders her to release it, consistent with her principle that ships must choose freely.
Zeiat departs to call a conclave, taking the Presger gun. Sphene's main body emerges from the Ghost Gate, and Fleet Captain Uemi, Breq's counterpart commanding forces in the neighboring Hrad System, arrives with warships, but Breq declines assistance. She convenes meetings with the system's AIs and officials to build governance for the new republic. Seivarden delivers a genuine apology to Ekalu, who accepts but keeps Seivarden waiting before fully reconciling. Breq introduces Queter, a citizen she helped free from detention, to Sphene, hoping the ship that wants a captain might find one in her. The novel closes with Breq reflecting that there are no true endings, only the next step, the next morning, the next bowl of tea.