Six million years before the main events, Abigail Gentian grows up in a sprawling mansion on a small planetoid in the Golden Hour, a torus-shaped region of human civilization orbiting the Sun in roughly the 31st century. Her mother, whose mental health deteriorated due to guilt over clones she created for an interplanetary war, believes ghosts pursue her; the house is perpetually expanded to keep those phantoms at bay. Abigail's only friend is a boy from another wealthy family. She introduces him to Palatial, a mind-interfacing game that immerses players in a fantasy kingdom by scanning their brains, and the game increasingly dominates their friendship.
In the novel's present, set millions of years after Abigail shattered herself into nearly a thousand clones called shatterlings who circumnavigate the galaxy in individual starships, two shatterlings narrate in alternating chapters. Campion and Purslane are members of Gentian Line, one of many Lines in a loose alliance called the Commonality. Every 200,000 years the shatterlings reconvene to exchange recorded memories called strands. Campion and Purslane have been secretly traveling together, a forbidden practice called consorting, and are decades late for the reunion. Campion carries Doctor Meninx, an aquatic scholar who denies machine sentience, whom he was supposed to deliver to the Vigilance, an ancient archive civilization. Instead, he seeks a ship dealer named Ateshga, hoping to upgrade his aging ship, Dalliance.
Ateshga lures them into a trap. Purslane secures their release by proving their Gentian identity and threatening retaliation. Among Ateshga's prisoners is Hesperus, a golden-skinned envoy of the Machine People, the galaxy's other major civilization. His memory has been severely damaged, and his left arm conceals a mystery: Beneath the golden plating grows a fully organic human forearm, which Hesperus theorizes was meant to help him infiltrate the Vigilance, which bars machines, though his damaged memory prevents confirmation. The shatterlings negotiate his release and depart. During the voyage, Doctor Meninx dies from a failure of his life-support tank.
The ships' emergency systems wake Campion and Purslane after detecting a Gentian distress signal. A recorded message from Fescue, a senior shatterling, reveals that the reunion was ambushed with Homunculus weapons, devastating armaments supposedly decommissioned by Marcellin Line millions of years earlier. Over 800 shatterlings were destroyed and the reunion world obliterated. Fescue warns latecomers to follow the Belladonna protocol for locating a secret fallback world. Despite the warning, Campion enters the debris cloud and finds Mezereon, a shatterling who has been hiding with four other survivors and four prisoners from an ambusher vessel. One prisoner, Grilse, a rogue Marcellin shatterling, claims the ambush was Campion's fault. During the rescue, Hesperus draws fire from a Homunculus weapon and is struck; his body fuses with wreckage, leaving him barely alive. He manages to communicate that they should head to Neume, their fallback world.
The survivors reach Neume, an arid world whose inhabitants, the Witnesses, are tall, fur-covered humanoids who worship the Spirit of the Air, a posthuman machine intelligence inhabiting the planet's atmosphere for millions of years. Betony, an ambitious shatterling, leads the 45 survivors already present, and Campion and Purslane bring the total to 52. Two Machine People are also among the group: Cadence and Cascade, brought by a shatterling named Sainfoin. The survivors debate censure for Campion and Purslane's consorting and investigate the ambush. Cyphel, an admired shatterling, volunteers to reconstruct Campion's deleted strand by pooling fragmentary memories from other survivors. The strand is critical because Grilse claimed it triggered the ambush. Campion theorizes that his visit to the Vigilance, where a curator discussed the Absence, the mysterious disappearance of the Andromeda galaxy, contained information threatening enough to provoke the attack.
Purslane and Campion bring Hesperus to the Spirit, a vast swarm of tiny flying machines, which disassembles him entirely and returns him the next day restored but apparently no more alive. Meanwhile, Cyphel is found dead, pushed from a tower balcony, and the shatterlings realize one of their own is a murderer. Cadence and Cascade examine Hesperus and claim he can only be repaired in Machine Space, prompting Betony to orchestrate a vote giving them Silver Wings of Morning, Purslane's ship and the fastest in the fleet, for the journey.
Aboard Silver Wings during the handover, Hesperus suddenly comes to life and reveals that Cadence and Cascade have been trying to kill him, extracting his memories during each examination. The Spirit not only restored him but merged with him: Hesperus now carries the consciousness of Abraham Valmik, the ancient human mind that became the Spirit over millions of years. The robots seize control of Silver Wings and accelerate away from Neume. Purslane and Hesperus take refuge in a white ark, an ancient converted generation ship stored in the cargo bay.
Hesperus reveals a buried truth: Millions of years ago, before the Machine People existed, a first wave of machine intelligence arose. The Lines of the Commonality, fearful of these machines, secretly implanted a neural weapon as a contingency. The weapon accidentally activated, driving the First Machines to extinction. The Lines erased all evidence at successive reunions and created the House of Suns, a secret Line ensuring the truth never resurfaced. The Vigilance's anomalous discoveries, combined with Campion's strand, threatened to expose this history, triggering the ambush. Hesperus fights Cadence when she breaches the ark, dismembering her but sustaining severe damage.
Campion leads a pursuit from Neume. Silver Wings heads not toward Machine Space but toward a Gentian stardam, a containment shell around a dying star, 62,000 light-years away. A signal from Neume identifies Galingale, another shatterling, as the House of Suns infiltrator who orchestrated the ambush and murdered Cyphel. Evidence comes from Grilse's interrogation and from Cyphel herself, who moved her rings between hands during her fatal fall to signal foul play. Galingale is captured after Betony sacrifices himself to stop him. Galingale reveals the stardam conceals not a dying star but a wormhole built by the Priors, an extinct precursor civilization, linking the Milky Way to Andromeda. The First Machine survivors fled through it millions of years ago. The Absence is simply a causality-preserving barrier between the two galaxies. Cadence and Cascade intend to open the stardam with a single-use opener hidden aboard Silver Wings.
Aboard the ark, Purslane discovers the opener, a string of eight linked brass spheres, but cannot prevent its activation. The opener sends its signal to the stardam. Silver Wings threads through the opening wormhole with Dalliance in pursuit.
Interspersed throughout the novel, further chapters trace Abigail's path to founding Gentian Line. After Palatial malfunctions and nearly traps her permanently, she decides to enter the cloning vat as the thousandth shatterling, her identity hidden even from herself. Madame Kleinfelter, her guardian, urges delay, but Abigail refuses. Kleinfelter's parting request is that whichever shatterling Abigail becomes should "try to be a good girl again, just once."
Campion wakes from abeyance in Andromeda. The galaxy appears normal from the inside, but the Milky Way is shrouded in its own Absence. He finds Silver Wings wrecked near a planet inside a colossal structure built by the First Machines. On the surface, the last remaining First Machine, a figure of thousands of glass marbles, explains that the First Machines have forgiven humanity and departed through further wormhole links toward the Boötes Void, a vast empty region of intergalactic space. The figure urges Campion to build trust between humans and the Machine People. It then leads him to Hesperus's body, melted and fused into a golden sarcophagus: Hesperus sacrificed his remaining consciousness to reshape himself into armor that protected Purslane during their crash landing, 17,500 years before Campion's arrival. Purslane is alive inside, in a coma but unharmed. The glass figure helps Campion begin to open the golden shell.