In the Hub system, the center of the Interdependency, Emperox Attavio VI is dying. After the tragic death of his son Rennered in a race, Attavio selects his bastard daughter Cardenia Wu-Patrick as his heir, a role she has never been prepared for. After Attavio's death, Cardenia is crowned Emperox Grayland II, following her father's dying advice. Just as she walks out onto the palace balcony to address the throngs waiting for her, a bomb explodes, wounding her and killing a number of people, including her best friend and chief of staff Naffa Dolg. All evidence points to the rebels of End. All the while, everyone around her strongly encourages her to consider a political marriage to Amit Nohamapetan, a member of an influential noble House.
House Lagos starship Yes, Sir, That's My Baby arrives to End to try to sell citrus fruit, only to be told that their license to sell has been suspended due to an outbreak of a crop virus on the planet that has been, allegedly, traced to the Yes, Sir's sister ship No, Sir, I Don't Mean Maybe. Lady Kiva Lagos, the representative of her House aboard the Yes, Sir, goes down to the planetary surface to speak to the Duke of End. In the Duke's office, she encounters Ghreni Nohamapetan, an old lover of hers and a representative of a rival House, who manages to convince the Duke to turn away Kiva's thinly-veiled attempt at a very large bribe. With their long trip to End coming up empty, putting their profit margin deep in the red, Kiva comes up with a plan to make money off the rebellion on End. She charges exorbitant fees to allow the wealthy of End to book passage on the Yes, Sir to Hub. The scheme works, and House Lagos actually makes a profit on the trip.
On the planetary surface, Lord Marce Claremont, son to the Count of Claremont (a province on End), is summoned by his father, along with his sister Vrenna. The Count, a Flow physicist like his son, explains that his studies of the Flow over the past several decades have paid off. He's now convinced the Flow links between the Interdependency systems are going to start collapsing shortly, which will lead to the end of the Interdependency. Moreover, since the interstellar community is deliberately kept from being self-sufficient, the vast majority of the colonies will die out in a matter of years, or even months. With Earth cut off from the Interdependency for over a millennium and End the only other known habitable planet, the people of End are likely the only ones to survive the catastrophe. The Count charges Marce to leave immediately for Hub (a nine-month trip) in order to deliver the information to the Emperox and to avoid being stuck on End, when the End->Hub link collapses in a matter of days. Ghreni Nohamapetan visits the Count and asks that the Count redirect imperial taxes to help the Duke buy back the weapons taken by the pirates. Ghreni offers Kiva a substantial amount of money to let him know if any member of the Claremont family attempts to book passage aboard the Yes, Sir. When Marce tries, she does that but then also lets Vrenna know about Marce's kidnapping, allowing Vrenna, a former imperial marine, to rescue her brother. With Kiva's help, Marce boards the Yes, Sir under the guise of a crewmember, but the ship is intercepted near the Flow shoal by a pirate vessel (the same one that took the weapons). The pirates have been hired by Ghreni to recover an agent of his aboard the Yes, Sir, who is supposed to either take Marce alive or kill him. The attempt fails, and the Yes, Sir manages to enter the shoal.
As it turns out, the Nohamapetan siblings (Amit, Nadashe, and Ghreni) are aware of the changes in the Flow, except the scientists they employ has made a mistake and concluded that the Flow links are simply shifting, with End supposedly set to become the new hub. Hence Ghreni's attempts to subvert the Duke's power on End in order to become the Duke of End himself. Ghreni meets with the Duke and the Count and assassinates the Duke, managing to shift the blame to the Count, who then reveals to him the truth about the Flow. The commander of the imperial garrison agrees to Ghreni's proposal to make him interim duke in order to quell the rebellion, which Ghreni does in about 20 minutes, since he was the one who financed it anyway.
Upon arrival to Hub nine months later, Marce requests an audience with the new emperox, who grants him one, having learned about the Count's research from the holographic memory record of her late father. He confirms the worst - the Flow links are collapsing, and the colonies must prepare if they are to survive. Meanwhile, Kiva meets with her mother, Countess Huma Lagos, and tells her everything that has gone on in the End system. Together, they visit Amit Nohamapetan and blackmail him with the information, making large demands on the House of Nohamapetan. Cardenia meets Amit aboard a newly-christened ship of the House of Nohamapetan in order to tour it. During the tour, a shuttle slams into the ship, killing most of Cardenia's guards and Amit. The Emperox herself manages to survive, but barely. The evidence points to House Lagos, but further investigation by Kiva reveals House Nohamapetan as the culprit. Apparently, Nadashe was perfectly willing to sacrifice her brother in order to ensure the ascendance of her House.
Marce and Cardenia confront Nadashe at the meeting of the executive committee, where Marce reveals to the gathered officials the truth about the Flow. Nadashe is arrested, but not before she sends a message to a warship that immediately heads to End (the Hub->End link is still open and will be, in fact, the last to close) in order to secure the system for House Nohamapetan. Everyone assembled realizes that End is about to become the most important place in the known universe, being the only accessible habitable planet, where people can survive without life support systems.
Marce and Hatide tell Cardenia that a Flow link to Dalasýsla, which closed 800 years ago, has temporarily reopened. They wish to travel to that system to get an idea of how the isolation affected the artificial habitat. After sleeping with Marce, Cardenia gives them a ship. They travel to Dalasýsla and are shocked to discover that a few thousand Dalasýslans (out of millions) are still alive, eking out a miserable existence in habitats, put together from scavenging anything they can. They also learn that another ship has visited the system 300 years before them. They locate the ship and manage to reactivate its systems. The ship, the Auvergne, is home to the Virtual Ghost of its former owner, Tomas Reynauld Chenevert. Tomas tells them that he comes from a planet called Ponthieu in a star polity called the Assembly. Marce learns that the Independent Systems, which eventually formed the Interdependency, were one of three main interstellar polities, the other two being the Earth Empire and the Assembly. At some point, the extremists of the Independent Systems initiated the Rupture, which cut the Independent Systems off from the other settled worlds. Another ship enters the system and destroys the ship Marce arrived in, with Hatide being one of the casualties. The Auvergne manages to disable the enemy. The enemy crew of the ship The Princess Is in Another Castle reveals that they are mercenaries, hired (indirectly) by Countess Nohamapetan to kill Marce. They agree to testify in exchange for being rescued. Marce decides to leave the Princess for the Dalasýslans to salvage and takes the Auvergne back to Hub.
Kiva Lagos, who has been given control of House Nohamapetan operations in the Hub system, uncovers deep-seated corruption and exposes it to Cardenia.
Meanwhile, Cardenia decides to follow the example of the Prophet-Emperox Rachela I and declares that she had a vision of the Flow collapse, causing a political and theological crisis. Nadashe, who is in prison awaiting trial for a multitude of crimes, is freed by her mother, who fakes Nadashe's death. Countess Nohamapetan then starts planning a coup with two members of the House of Wu: Jasin and Deran. The plan is to bloodlessly remove Cardenia from power and replace her with Jasin, who would then marry Nadashe. Deran would then take Jasin's position as the director of House Wu's business operations. They also try to convince Archbishop Korbijn to use Cardenia's "visions" as a pretext to initiate a schism in the Church to remove the Emperox as its official head. Cardenia learns of all this from Jiyi, the AI that runs her Memory Room. Apparently, Rachela I programmed Jiyi to seek out information throughout the Interdependency's computer networks, which people wanted to keep hidden. In addition, Deran Wu offers to turn state's evidence against the conspiracy in exchange for Jasin's position.
Cardenia invites all members of the conspiracy to a banquet (attendance mandatory), shortly before her scheduled appearance before the Parliament (everyone expects her to declare martial law). There, she puts Kiva on her Executive Committee (despite Kiva's protestations). Archbishop Korbijn confirms Cardenia's visions as being in line with the Church's doctrine. Cardenia then has all members of the conspiracy arrested on charges of treason, although Nadashe manages to escape. Also, a number of the warships that were to take part in the coup flee to End to reinforce Ghreni's hold on the system. Cardenia asks Marce to come up with a way of sneaking ships into the End system.
Marce figures out that an evanescent Flow shoal will open from House Lagos's home system to End in six months and informs Cardenia. She summons her commanders and asks them to assemble a fleet to retake End from the Nohamapetans using this back door and to allow refugee ships to get there. Marce then remembers what happened to the Tell Me Another One and realizes that moving and expanding shoals are possible. Cardenia tells him that she has access to the Flow science from before the Interdependency that was used to initiate the Rupture but she refuses to share it with him out of fear that someone may misuse that information. They have a fight over it.
Kiva Lagos has been managing House Nohamapetan's finances and learns of the conspiracy against the Emperox. She and Cardenia fake Kiva's fall from grace, so Kiva's attempt to join the conspiracy looks believable. But Nadashe has no intention of letting Kiva in. She seemingly has her killed, while actually whisking her away onto a smuggling ship bound for Bremen, where Kiva is kept as a prisoner. Countess Huma Lagos dismisses the idea that her daughter is really dead. Kiva manages to get the ship's crew to mutiny against the captain.
After Cardenia finally gives Marce the data, he leaves with Tomas to observe a new evanescent shoal in the Hub System. Before he leaves, Cardenia proposes to him and he accepts. Meanwhile, Tomas has figured out that Jiyi is actually Prophet-Emperox Rachela I's Virtual Ghost, who has been secretly watching events unfold for over a millennium. He informs Cardenia, who confronts Rachela, who reveals the latest plot against her.
Several days later, Cardenia is killed by a bomb during a meeting with one of the conspirators. Since she has neither produced nor named an heir, the decision falls to House Wu's executive committee. Proster Wu tells the Archbishop of Xian that they have chosen Nadashe. The Archbishop resigns rather than crown someone like that. Church rules state that a meeting of bishops is required to select a new archbishop, which will take at least a month. Until then, Nadashe can't be crowned.
When Kiva returns from Bremen, she is taken to see Nadashe, who has moved into the imperial palace. Nadashe offers her a large sum of money and rulership over her house in exchange for the support of House Lagos. Kiva refuses and is imprisoned under an a fake name. After some time in prison, Kiva is sprung by someone, and she assumes it's her mother's doing.
After a month, the new archbishop is chosen, and the day of coronation arrives. In the middle of the ritual, everyone at the cathedral suddenly sees a holographic projection of Cardenia, who reveals the entire conspiracy, including her own murder at Nadashe's hands. She also explains that shortly before her death she officially named Kiva as her successor, although that was kept secret in order to protect Kiva. Just then, Kiva walks in and tells Nadashe to move from her spot. Cardenia also reveals each house's proprietary secret to the entire Interdependency, thus ending their monopolies.
Nadashe and the entire conspiracy is arrested. Cardenia's Virtual Ghost explains to Marce why she had to do what she did (i.e. allowing her own death), knowing that she was choosing the Interdependency over their relationship. Had she simply foiled that conspiracy, there would have been another, and another. Kiva, the new (and last) emperox, follows Cardenia's suggestion and has House Wu and House Nohamapetan dissolved and their holdings placed in the trust of their subjects. Cardenia intends to make sure that as many people as possible survive and end up in the End System, and Marce's research may be the key to making Flow shoals move and expand in order to allow entire habitats to be moved to End.
Cardenia tells Marce that he can either go back to End as its new duke or take a Flow shoal that will appear soon, which will allow him to go to a system that was at one point claimed by the Earth Empire. Marce chooses the latter, and Tomas goes with him, although Cardenia makes the latter promise to bring her beloved to her, no matter how long it takes.