Summary of Chapter 1
Along with every other sixteen-year-old in the city of Atlantia, Rio and her twin sister Bay have come before the Minister in the Temple. Today is when they make the choice of where they will live out their lives: Below, in Atlantia, a fully functioning city deep under the ocean; or Above, on an earth blasted by radiation and environmental degradation. People living Above eke out short lives providing all of the necessities for the people living Below in Atlantia. However, life Above does have its benefits - one has complete freedom of movement and enjoys the possibilities of adventure and discovery, unlike the people Below who never even see the sun.
Bay tells Rio that today will be particularly hard, and Rio assumes that is is because the new Minister has come to replace their mother, Oceana, who died six months ago. The two girls lost their father from water-lung when they were infants, so they are now orphans.
Bay asks if their mother's sister Maire will be here today, but Rio shushes her harshly as the Minister Nevio begins the sacred ceremony. Each teenager steps forward and makes his or her choice to stay Below or go Above. A boy named Fen Cardiff is one of the first to choose to go Above, eliciting a cry from someone in the audience. Rio considers him with a twinge of jealously. She has always wanted to go Above, but her sister Bay has made her promise to stay Below so that the two will not be separated. They cannot go Above together, because one person from each gene line must stay in Atlantia.
Rio steps forward and chooses to keep her promise to her sister, though she knows she will regret it for the rest of her life - she will stay Below. Bay comes next, and shockingly, says she will go Above. Immediately peacekeepers surround Bay and rush her off to the transport - those who choose to go Above are not given time to say goodbye to their families. Stunned, Rio tries to follow her sister. A friendly priest named Justus takes her arm, but she says "No" in her real voice, and he lets go of her with alarm. When she looks up, Bay is gone forever. No one returns from the Above, and no one who has chosen the Below is allowed to go there.
Summary of Chapter 2
Rio wanders the streets of Atlantis in a daze, walking by the air-sellers and merchants like a sleepwalker. Certain that her sister would not leave without an explanation, she tears apart her sister's room looking for a note. However, she finds nothing. Rio is puzzled by her sister's actions - Bay would never do anything so rash and cruel without a reason. She tries to think of a way to get to her sister, but all of the transports to the Above are carefully guarded.
So Rio continues to wander the streets of Atlantia. She meditates on the history of the city; it was constructed as a refuge after a time of terrible environmental degradation. Modeled after other ancient cities, Atlantia is formed by a series of enormous enclosed bubbles. Nearly all the materials are artificial, and wood is particularly valuable. However, the residents of Atlantia have designed synthetic trees out of metal to beautify their city. Transportation around Atlantia is provided by a complex system of gondolas.
Rio passes by a vendor selling masks and notices one modeled after a sea witch. She recalls a conversation she once had with her mother, in which Rio mentioned that she'd heard her aunt Maire was a sea witch. Her mother seemed alarmed and scolded her sharply. This mystery is deepend by the fact that Rio's mother's body was found on Maire's doorstep the night she died.
Maire is almost certainly a siren - a woman who can use her voice to convince others to do her bidding. Rio is as well, a secret that she, her mother Oceana, and her sister Bay have kept from the rest of the world. Though believed to be a miracle, sirens are taken from their families of origin, and Rio's family could not bear to lose her.
Rio visits the swimming lanes where her sister Bay used to compete. She asks the organizer, Aldo, if her sister left anything, and he says that she has not. Rio also decides that she will start competing in swimming races in order to earn money; though her work at the Temple pays her room and board, she needs to earn a bit of cash to support herself.
As Rio is leaving the swimming lanes, she hears an unexpected and unwelcome voice - her aunt Maire, who tells her that she knows Rio is a siren and she needs to speak with her about her mother and sister. Because Rio suspects her of causing her mother Oceana's death, she is unwilling to trust her. However, Maire tells her that she can help Rio get Above - before it is too late.
Summary of Chapter 3
Rio takes refuge in the temple. Not only does this place hold reassuring memories from her mother's time as minister, it also means that Maire cannot pursue her here - sirens have their own place of worship elsewhere in the city. The sirens' lives are strictly controlled because of fear that they will use their substantial powers for evil.
Rio lights a candle for the gods, whose statues are based on different animals from the Above, including tigers. She meditates on her own abuse of her powers as a young child; she often made Bay do what she wanted, even if it made her cry. Rio's mother was immune to her siren voice, and gently trained her daughter to control her power and hide it from the public. Rio begins to weep.
A young machinist sits down next to Rio, introducing himself as True Beck. He explains that his best friend Fen Cardiff also left for the Above, and that he saw Fen with Bay more than once. Rio is annoyed at this stranger for intruding on her personal space, and dismisses the notion that Bay would have met with a young man so many times without telling her. True asks Rio to help him find out why they both left, and asks her to meet him at the deepmarket. She does not reply.
Back in her room, Rio lies in bed listlessly, mourning her sister. She has nothing to keep her in Atlantia any longer, but she has no way to leave - no one has been able to steal a transport before. She ponders Maire's offer, and wonders if she really is the evil sister that she appears to be. Rio comes to the conclusion that she must get to the Above, by whatever means necessary.
Atlantia begins with a scenario common to other contemporary young adult novels: a sorting process (other examples include The Hunger Games and Divergent). The result of this sorting process is usually not something that the main character expects, and she will experience the consequences of this situation throughout the rest of the novel.
Though Rio blames Maire for her mother Oceana's death (not unfairly - Oceana was found dead at Maire's doorstep), Maire is actually her greatest protection: officials believe that there can be only one siren in any family line, and since Maire is a known siren, no one suspects that Rio is as well. If Rio is known to be a siren, she will be taken from her family and raised by the Council. This policy was instituted when sirens began to abuse their powers for their own gain, and the Council wants to make sure that they are educated properly to use their abilities for the benefit of everyone in Atlantia. However, taking children away from their parents seems like a cruel way to offer an education.
The names of Rio and her family members are derived from words used to refer to bodies of water, a significant theme in the novel. Maire's name resembles the Latin word for "sea" ("mare"). "Rio" means river in Spanish and Portuguese. "Bay" is an English word referring to a body of water enclosed on three sides by land but connected to a larger lake or ocean. Oceana's name closely resembles the English word "ocean." The names of these characters also demonstrate elements of their personalities. Rio is drawn to both the Above and the Below, and rivers run along the surface of the earth. Oceana is known for her depth and compassion, and Bay is closely connected to her mother.
This section contains numerous allusions to Hans Christian Andersen's story The Little Mermaid. As in Andersen's story, there is a girl from the ocean longing to see the human world, a struggle surrounding voice, and a mysterious sea witch who may help the protagonist or may destroy her.
Maire's ominous comment, "Can't you hear the way the city is breathing?" (32) is an example of foreshadowing, suggesting that some kind of great catastrophe is about to befall Atlantia. Could this be part of the reason why Bay suddenly left the city?