In a future where the atmosphere is full of Aether — strong electrical currents that burn anything they touch — people have separated into two groups. The Dwellers live in protective pods to escape the storms and the Outsiders do not.
Aria, a 17-year-old Dweller, lives in a pod named Reverie. She and her fellow Dwellers spend their days in the Realms, virtual worlds where they can experience anything from a forest to Ancient Rome. Pain and fear don't exist in the Realms because there are no consequences in the virtual world. They see these lives through Smarteyes, clear screens that attach to their skin around one of their eyes. The screens also send electrical impulses to the brain to trick the brain into thinking it can smell, taste and touch things in the Realms.
Aria's mother, Lumina, is a scientist working and living in the pod named Bliss, but communication with Bliss has been cut off, leaving Aria to fear the worst. To learn what's happened to her mother, Aria flirts with a boy named Soren, the son of the head of security for the pods.
When Soren suggests that Aria and some of his friends break into a broken agriculture dome, Aria agrees, hoping she can use the chance to convince Soren to help her. Soren shuts off everyone's Smarteyes so they won't be tracked when they break into the dome. Inside the dome, Soren and his friends become manic and start a fire that begins to burn the trees and plants growing there.
Aria tries to escape, but Soren pursues her. After Aria restarts her Smarteye, it begins recording what's happening. Soren wrestles Aria to the ground and rips off her Smarteye, causing her to bleed. In the seconds before he takes the screen, Aria sees that she received a message addressed to "Songbird." She knows the message is from her mother, since Songbird is Lumina's nickname for Aria. With the screen gone, Aria is disoriented and passes out, but not before she notices an Outsider watching her.
The Outsider, known as Perry, broke into the dome when Soren disabled the security system. Soren attacks Perry, but Perry easily knocks him unconscious. Perry is a Scire, a person born with a heightened sense of smell. This power allows him to read a person's emotions from their scent. He is also a Seer, someone with a heightened sense of sight, though his power as a Scire is stronger.
Perry sees that the fire is growing and will soon destroy the dome, so he moves Aria to safety. Noticing Aria's Smarteye on the ground, he grabs it and puts it in his pack. He intends to leave the device with her but forgets. With Aria safe, he leaves the pod and begins his journey home. It takes him four days to travel back to the Tide, the tribe where he lives.
Perry returns to his brother's home in the middle of night. As Perry lies down in Vale's house, Vale's son, Talon, comes to see him. Talon is dying from an illness that killed his mother a month before. The sickness is progressing, taking Talon's strength and some of his mobility. Perry is bonded to Talon in a way that the Scires call "being rendered." When Perry scents Talon's emotions, they become his own. He always puts his nephew's well-being above his own.
Aria wakes in an unfamiliar room wearing a medical suit that's used to heal the sick and injured. Dr. Ward, a man who worked with Lumina, tells Aria that her only injury is a laceration on her forehead. He also tells her that the only other person to survive the fire was Soren, though he was badly burned and his jaw was broken.
The Consuls, the men who make up the government, want to talk to Aria about the fire, so she is brought to a room where Consul Hess, Soren's father, is waiting. He tells her that another Consul is with them via Hess' Smarteye, and that he's recording their conversation for the other Consuls to watch later. After Aria describes what happened, Hess tells her that Soren's story was different: He said it was Aria's idea to break into the dome.
Aria denies this, saying that her Smarteye's recording will show the truth once it's found. When their meeting ends, Hess tells Aria that he's arranged for her to travel to Bliss to be with her mother. Aria boards a hovercraft with a group of guards, but less than an hour into the journey, the guards throw Aria out of the hovercraft and leave her in the Outside.
Back where the Tides live, an Aether storm is gathering. As the tribe watches the stormy skies, Vale returns with a huge deer. Vale is the Blood Lord, the leader of the tribe. Perry hasn't brought in any large game, so he is jealous of Vale. The bad blood between the brothers causes them to argue in front of the tribe. Perry knows they've overhunted the land and that the growing Aether storms will likely destroy the tribe's home. Vale refuses to move his people and criticizes Perry's ideas. Before the disagreement escalates, Talon asks Vale if he and Perry can go hunting. Vale agrees, so Talon and Perry hike to the ocean to shoot seabirds. Perry tells Talon that he can't stay with the Tides anymore. He knows the rift with his brother will lead to one of them dying, and he wants to spare Talon the pain that would cause.
They're interrupted when Dwellers in hovercrafts arrive and grab Talon. Perry kills some of the Dwellers as he fights them, but they still flee with Talon. One of the Dwellers knows Perry still has Aria's Smarteye and demands that Perry turn it over. After Perry kills the guard, he returns to the Tides with the Smarteye still in his possession. He tells the Tribe that Talon has been captured, probably in retaliation for the dome break-in, and he promises to find him. Vale warns that any action Perry takes could result in the Dwellers annihilating the tribe, and he tries to attack Perry. Perry dodges the blow and runs away.
Meanwhile, Aria is wandering through the Outside when an Aether storm begins. As the storm grows closer, Perry finds Aria by catching wind of her scent, which reminds him of the scent of violets. As they run together to escape the storm, Aria hurts her foot, but they manage to take shelter in a cave. Because Aria doesn't trust Perry, she tries to escape but passes out before she makes it very far. Perry brings her back into the cave, where Aria remains unconscious for two days.
When she comes to, Perry asks why she was out of the dome. Aria tells him that the Consuls thought she let Perry into the dome. When she asks why he saved her from the storm, Perry reveals that he wants information to help him free Talon. He's willing to trade the Smarteye for her help. Aria agrees, but when she tries to use the Smarteye to contact Lumina, she realizes it isn't working. Perry's friend Marron can fix the screen, so the two decide to travel to Marron's home. To protect Aria's feet, Perry takes the leather cover of a book and makes makeshift shoes.
Perry and Aria spend the next two days traveling, and Aria tells Perry about the Realms. After their third day of hiking, they find another cave to take shelter in. When Perry leaves to hunt, Aria decides to gather berries. She returns to the cave and finds three men there.
They seem friendly, so when they invite Aria to leave with them so they can share their meal with her, she agrees. Perry arrives before they have left. He kills the men, and then tells Aria that they were from the Croven tribe of cannibals and that they planned to eat her. She doesn't believe him and calls him a monster. Angry because of her unkind treatment, Perry points her toward Mount Arrow, their next resting point, and leaves her to fend for herself. At Mount Arrow, Perry takes shelter in an abandoned house and waits for Aria to arrive. It takes her a few hours, but she makes it to the house and falls asleep.
In the morning, Aria discovers she's bleeding. She thinks she's dying, but Perry tells her that she's begun menstruating. Aria is shocked because Dwellers don't menstruate. Procreation happens through genetics, and doctors control hormones to prevent women from having a period. Perry believes the Croven will retaliate, so they gather their supplies and keep traveling.
The next night, Perry catches the scent of his friend Roar, an Aud — someone with a powerful sense of hearing. When Roar touches someone, he can hear the person's thoughts. After Perry tells Roar that the Dwellers took Talon, Roar agrees to help rescue the boy. Accompanying Roar is a boy named Cinder.
Cinder doesn't like Perry because he's a Scire. When Aria discovers what a Scire is, she's angry that Perry didn't tell her he could sense her feelings. Aria keeps her distance from Perry the next day and stays close to Roar. Roar is able to hear a group of Croven tracking them. Perry doesn't want the Croven to capture Cinder, so he tells the boy to go. When the boy refuses, Perry threatens to shoot him with an arrow if he doesn't leave.
Without warning, Aether begins burning from Cinder, as if it's flowing through his veins. Some of the Aether burns Perry's hand. The attack weakens Cinder, but Perry refuses to leave the boy behind. They have to carry him as they hike up the mountain. The Croven are close, forcing the group to run. Perry and Roar send Aria and Cinder ahead to Marron's home while they stay behind to keep the Croven at bay. After Aria and Cinder make it to Marron's compound, they tell him that Perry and Roar need help. Marron sends reinforcements, and with their help, Perry and Roar escape the Croven.
As the group rests and receives medical attention, Cinder feels guilty about attacking Perry and is afraid that the Aether in him, which he can't control, will hurt someone else. He leaves the compound when no one is looking. High, thick walls that make it one of the last safe places in the area surround Marron's compound, called Delphi. Marron has filled his home with relics from the time before the Aether storms destroyed the outside world. He also has electronics that will help him fix Aria's Smarteye.
Aria tells Marron about her mother's message on the Smarteye and the video of Soren's attack that she needs to prove her innocence. When she tells him that her mother was working in Bliss, Marron says he heard a rumor that Bliss had been destroyed by an Aether storm. Later, Perry tries to comfort Aria in her room, and Aria asks him to stay with her for the night to keep her company. He agrees and sleeps on the floor next to her bed.
The next day, Marron manages to fix Aria's Smarteye. They watch the video of the incident in the agricultural dome and find the "Songbird" file, a video message from Lumina. She reveals that the secret research she's been doing in Bliss has to do with the limbic system of the human brain, the part that controls fear, decision-making and the urge to procreate. Lumina found that prolonged exposure to the Realms made this portion of the brain deteriorate. This resulted in people who confused pleasure and pain, fear and excitement.
The disorder is known as DLS. Lumina was trying to find a cure and had begun experimenting on Outsider children. She reveals that Aria's father was an Outsider, making Aria part of both worlds. When Perry realizes that Talon might be one of the children Lumina is experimenting on, he storms out of the room.
Aria tries to use the Smarteye to enter a Realm and speak to her mother, but her access is denied. Aria convinces Perry to try entering the Realms, thinking that because his DNA isn't in the system, Marron might be able to hack into the Smarteye and allow Perry access. When Perry agrees to try, he manages to find Talon. The boy, who was dying in the Outside, is happy and healthy in the Realms. Talon tells Perry that Vale is in the Realms with him. Before Perry can learn anything more, he has to leave the Realm or risk being caught. With Vale gone, Perry realizes he will be Blood Lord. He agrees to take Aria back to Reverie, and then he will return to the Tides.
The Croven still want revenge and have gathered outside the compound, preventing anyone from leaving. Perry suggests leaving during an Aether storm since the Croven will be seeking shelter. While Aria, Perry and Roar wait for a storm, Roar teaches Aria how to fight with a knife. After a few days, a storm begins and the three leave with a few of Marron's men.
Croven scouts spot them, and the cannibals kill Marron's men and wound Roar. As the Croven surround the group, Cinder shows up. Using the Aether flowing in his veins, he incinerates the Croven. Cinder and Roar return to the compound, while Aria and Perry continue to Bliss. That night, a pack of wolves begins to chase them, so they find an abandoned tree house and make it inside before the wolves catch them. Perry is in love with Aria now, and she feels the same way about him. Their conversation culminates with them having sex.
After a few more days of travel, they reach Bliss, only to find it surrounded by guards. Aria tells Perry that he must return to the Tides and leave her in Bliss. He agrees, but helps her sneak inside by shooting out a floodlight so she can move around unseen. She steals a guard's uniform, makes it inside and finds Dr. Ward. He takes her to see Lumina, who was killed while trying to stop the outbreak of DLS in Bliss. While Aria is saying goodbye to her mother, guards enter and take Aria's Smarteye before knocking her unconscious. She wakes to find Consul Hess and Dr. Ward watching her. Hess tells her that he wants her to find the Still Blue, a place where the Aether isn't in the sky. She believes the Still Blue is only a rumor, but agrees to search for it when Hess threatens Perry and Talon.
Perry is upset about leaving Aria. After he comes across a group of men, he trades a dagger for a bottle of alcohol, gets drunk and fights a man named Reef. Perry wins the fight, but spares Reef's life. Because of this, Reef and his men swear fealty to Perry and return to the Tides with him. Perry is surprised to find that Vale is still with the Tides, not with Talon in one of the pods. Vale reveals that he's been selling children to the Dwellers in exchange for food. After Perry learns that Vale sold Talon and blamed Talon's disappearance on Perry, the brothers fight. When Perry kills Vale, he becomes the Blood Lord.
Aria leaves Bliss and travels to Marron's home. She makes Roar promise not to tell Perry that she was there, but asks him to give Perry a violet, the flower that reminds Perry of her scent. In the spring, she's still searching for clues to the Still Blue when she hears something. It's Perry coming to find her. The two reunite.