The story began when Rio attended the ceremony of the Divide. Rio wanted to go aboveground, but she promised her Below-loving twin sister, Bay, to remain belowground in Atlantia.
Rio did the ritual before Bay. She, as promised, accepted her fate Below. However, Bay surprisingly chose sacrifice Above. A priest comforted Rio, but she said “no” in her real, siren voice, one that she had hid since her birth.
Rio searched desperately for a written explanation to what Bay had done. She scrounged through her and Bay’s room, and walked to the swimming lanes Bay used to compete in. However, there was no clue. To distract herself from the mystery, she offered to take Bay’s place in the races.
When she was at the swimming lanes, Rio met her siren aunt, Maire, whom she had not seen since her mother’s funeral. Maire had heard Rio speak at the ceremony, and wanted to help her go Above.
Rio ran away to avoid her aunt. She was engulfed in the memories of her late mother, Oceana, who was the temple Minister. As she wept, she met True Beck, a boy whose best friend had also left mysteriously for the Above. True insisted they help each other solve the enigma of Bay and Fen’s departure to the Above. Rio rejected, and when she changed her mind, True was gone.
The next day, the current Minister, Nevio, wanted to talk to Rio. Nevio insisted that the temple was never where Rio belonged, and whisked her off to the mining bays, where he claimed was the place for her to best be.
When Rio finished her shift at the mining bay the next day, Maire found her outside the temple. Maire led her to the floodgates, where dead bodies were sent up onto the surface Above. Rio realized she could not go Above the way Bay did, but she could go through the floodgates, the way her mother did. Maire gave her a seashell, in which she could ask questions and Maire would answer.
After her encounter with Maire, Rio went to the swimming lanes. She had new purposes for racing: to grow strong enough to go through the floodgates, and to earn enough money to buy a pressurized air tank. Unfortunately, Rio could not race like Bay did. Rio decided to swim against herself. She swam while wearing her machinist’s work suit from the mining bays.
After swimming, Rio went to the deepmarket to search for True, who sold moving, metal fish. She told him she changed her mind about working together, and was inspired to entertain the bettors at the swimming lanes by dodging the fish. Nevio the Minister gave his sermon after the deepmarket closed early, in which Rio discovered his secret identity as a siren.
One day, when Rio was promoted, Maire found Rio after work. Rio discovered her ability to command non-living objects using her siren voice — an ability only she and Maire had. In a later discussion at Maire’s apartment, Rio learned why the sirens were hated — two sirens were arguing in the temple, and a few worshipers died while they argued. The pair of sirens were sisters, and there had never been two sirens in a family until Rio was born.
The next day, True gave Rio money so she would not have to swim in the lanes, thinking Rio wanted to buy back her mother's ring. Rio disagreed, but accepted the money. When she was back in her room, she talked to Maire through the seashell. Maire told her that the Council poisoned her mother because she knew too much.
A breach drill was announced at work. Rio forgot her air mask, which she was supposed to carry all day. After a while, a siren voice over the loudspeakers told her this was a real breach.
As the minutes passed, no water rushed in. The breach in the deepmarket had been sealed off. There were no survivors.True revealed that he also heard Rio speak with her siren voice on the day of the Divide.
The next day, it was announced that group burials would be held, since the death toll was too high. Rio took this as a chance to go Above through the floodgates. However, she failed. The water was lowered, and she was caught.
Maire met Rio in her holding cell. She signaled for her to tell the public about her identity as a siren. Maire wanted Rio to help the Below. When Nevio entered the room, Rio decided to listen to Maire. She spoke using her real voice, knowing it was the only way to go Above.
Rio was permitted to go Above with the other sirens. Maire gave Rio a letter from Bay. Bay explained the reason she went Above: Sirens could not survive long Above. She left to keep Rio safe.
True was escorted into the transport just before it began to ascend. True revealed that he was not a siren, but he could tell when a siren is lying.
When Rio was Above, Maire told her how to escape. The sirens sang in harmony. The sirens were shot down one by one. Maire gave Rio a seashell with her mother’s voice, and gestured for her and True to escape.
Rio and True swam to the temple of the Above. Rio met Bay, Fen (True's best friend), and Ciro, the Above Minister. Bay told her about the miserable life Above for the people Below.
The next morning, Ciro entered the storage room True and Rio were hiding in. He confirmed the death of all the other sirens, and told them about a showing of the sirens being held by Nevio and the Below Council. Rio decided to speak, too, at the viewing, despite the risk. Bay would descend Below with True and talk to the people there.
Rio woke up in the afternoon. Someone tried to unlock the door to the storage room. Bay and Fen hid in the back closet and locked it from the inside. Nevio and an Above Council member arrived. The temple bats, were brought Above and into the storage room. Nevio opened the closet, and dumped a dead Ciro and temple bat inside.
Rio made herself seen by Nevio. She spoke to the people Above. She was weakened by the Above, but when she was about to pass out, one of the bats came. Rio realized that the bats could provide her strength. She talked about Atlantia and the need to save the city. Hundreds of temple bats soared past Nevio to land on Rio. As the bats flew away, Rio felt the strength leave her.
When Rio woke up again, she was in the transport, going Below. Her speech worked.
Atlantia received reviews from the School Library Journal, Justine Magazine, Salt Lake City Weekly, and Shelf Awareness.
Atlantia was also reviewed by multiple noted authors, including Shannon Hale, who wrote, "“Utterly captivating. A heroine unlike any I’d met before, a setting I’d never glimpsed, a story I’d never imagined. Atlantia is fresh, wild, and engrossing. I love Ally Condie.”