Fifteen-year-old military prodigy June Iparis is on the run with Day, the 15-year-old guerilla revolutionary with whom she's fallen in love. June and a political group called the Patriots saved Day from being executed as a traitor to the Republic. June and Day travel by train to Las Vegas, the farthermost military outpost of the Republic. Day needs medical attention, and he believes they will be able to reunite with the Patriots.
June knows the Patriots will not help them without payment, and she has no money left to offer them. Day wants to make sure his former companion Tess is safe with the revolutionaries before he and June head to the Colonies. The Colonies are an area in eastern Colorado and the Dakotas. (The melting ice of Antarctica flooded much of North America.) The military-run Republic has been at war with The Colonies for as long as Day and June can remember.
Arriving in Las Vegas, June disguises herself as a prostitute. Day pretends to be her client. She wears a pin that she hopes will attract the attention of the Patriots. An announcement over the government-run Jumbotrons informs the people that the supreme head of the Republic, known as the Elector, has died. His son, a young man June once met, has assumed his father's position.
Before they have time to contemplate what this means, Day collapses from his wounds. Fortunately, Kaede, a leader of the Patriots, rescues the two. She agrees to take them to her barracks where they can meet her superior. Day is relieved to reunite with Tess in the barracks and learn that she has joined the group dedicated to bringing down the Republic.
Day and June are introduced to the Patriots' ringleader, a man named Razor. Day asks the group not only for medical help, but for aid in finding his younger brother, Eden, who's been infected with a plague and used as a biochemical weapon by the Republic to sicken the Colonies. Day also asks Razor to help him and June escape to the Colonies. Razor agrees, but only if the two of them pledge allegiance to the Patriots. After that, he will reveal the assignment they must perform as payment for the services they desire.
Out of options, the two agree. Razor tells them of the Patriots' plan to assassinate the new Elector and establish a new, less militaristic government. Day is immediately onboard with the plan, but June harbors some reluctance. She knows Razor must be a double agent as he lives in a Republic barracks. She also wonders who is sponsoring the Patriots' obviously well-funded organization.
Razor plans on having June return to the Republic. It seems the new Elector, Anden, had been attracted to her when they had met several weeks earlier. The reason for June's disappearance from the Republic isn't known. Many think she was taken prisoner by Day and used as a hostage. They're hoping June can convince Anden and the Senators that she is still loyal to the Republic. She will then help with Anden's assassination.
Day will be used to rally the people to the Patriots' cause, as he has become a celebrity of sorts. The common people of the Republic have always admired how he fought against the government, and rumors abound that he survived his "execution." As they prepare for their assignments, Day is surprised when Tess suggests that June should not be trusted. After all, it was June who initially turned Day in to the authorities. She may want to return to her privileged life. Day senses Tess' romantic attraction to him.
Day undergoes an operation to repair recent and past damage to his knee. His wounds are completely healed when he wakes up. He and June struggle to connect because of their different backgrounds, but physically, they are attracted to each other.
Day and Kaede are to disguise themselves as Republic soldiers and hide aboard an airship headed for the Capital city of Denver. June will allow herself to be taken prisoner and returned to the Republic where she will ask to meet with Anden.
She is shocked to see Thomas, a friend of her family's, with her dog, Ollie. She knows he is searching for her. Once a trusted ally, June knows Thomas is responsible for her brother's death. She resists arrest but is taken into custody. June insists on seeing the Elector. After an enlightening conversation with Thomas, in which she finds out more about her brother's death and the quarantine of her home city of Los Angeles, June learns she will get an opportunity to meet with Anden.
Kaede and Day make their way to the underground headquarters of the Patriots. Along the way, Kaede talks to Day about Tess, reminding him of how similar they are and the past they'd shared. Day realizes that he and Tess are much better suited for each other, but June is the person he loves.
Once at headquarters, Day meets other Patriots, several of whom are jealous of his celebrity status and relationship with Tess. He learns that he's the person they want to carry out the assassination of the Elector.
Although her arms and legs are shackled, June is dressed in a beautiful gown and allowed to dine alone with Anden in a dining hall, not a prison cell. She is surprised to learn he went incognito to the same university she attended and was the mastermind behind a famous prank. She finds him kind, sincere and in a precarious position. Although he inherited the title from his father, he is experiencing opposition from some Senators. He is trying to win the military, and the common people, to his side so that he can bring change to the government.
After proving her loyalty with a lie-detector test, Anden admits he needs her and Day to be on his side to win the people's approval and defeat the Senators. He promises to return Day's brother to him as a gesture of good faith. June begins to doubt whether Razor has been truthful with her, but continues with the Patriots' plan to execute the Elector until she can learn more.
Tess tries to convince Day that he's been brainwashed by June into believing everything she says. Tess' jealousy confuses Day, but he continues to believe June is on his side. His faith is tested when he sees what he believes is a video of the Elector and June kissing. In actuality, Anden is revealing his plans to release Eden and his hope of winning June and Day to his side.
At the end of the video, Day sees June give him a signal to stop. He wonders if the Elector has corrupted her or if she truly wants to stop the assassination plans. He doesn't have much time to contemplate the problem. He must make his first appearance as a soldier for the Patriots that night in a raid on a Republic train.
Day discovers a young boy infected with the same plague as his brother. Before he can rescue him, soldiers arrive, and Day must escape. Day is more determined than ever to save Eden from the Republic.
June wins the trust of the Elector and is pardoned of all crimes against the Republic by the Senate. June decides to try and thwart the assassination attempt. Although at first she plans to feign illness, she actually does feel sick when she fakes collapsing. Anden orders her taken to the hospital, but Cmdr. DeSoto, a.k.a. Razor, orders that the Elector follow his original route through the city.
June knows this will bring him directly into the Patriots' ambush. The soldiers throw grenades to stop the Elector's motorcade from passing. As Day waits to throw his explosive, June jumps from one of the cars and signals the Patriots to stop. As bullets and grenades go off around them, Day rescues June, and Anden is saved. Day tries to get Tess to escape with him and June, but she refuses, feeling betrayed by Day's actions.
June and Day argue as they travel through abandoned tunnels toward the Colonies. Day realizes June has no proof of Anden's promises, only her faith in him. He begins to think like Tess that June is a puppet of the Republic, but he doesn't abandon her. June gives him hand-to-hand combat lessons during which he discovers she has a fever.
They continue through the tunnels and finally making it to the Colonies. At first they are treated as unwelcome refugees, but then someone recognizes Day. June is taken to a hospital as her fever worsens. A crowd gathers outside the hospital, hoping to get a glimpse of Day, whose exploits in the Republic have given him celebrity status in the Colonies.
In the crowd, Day sees Kaede holding a sign that tells him he has to return to the Republic. He meets with her secretly and learns that June had been right to distrust Razor. The Republic's Senators blackmailed Razor into assassinating Anden. Razor would then be made the new Elector.
Kaede begs Day to return to the Republic before Anden loses his grip on the military and Razor overtakes the government. If Day throws his support behind Anden, people will rally behind him, too. Kaede then shows Day the truth about the Colonies. They aren't the utopia he'd dreamed they were. Instead, the poor and middle class are treated as badly as they are in the Republic.
While Day meets with Kaede, Colonial soldiers try to take June prisoner. Although sick, she manages to escape. Day and Kaede rescue her. They steal a fighter jet, which Kaede pilots toward the Republic. She manages to get them through the Republic's defenses, but a stray bullet kills Kaede immediately after they crash land in Denver.
The city is already on the brink of revolution. Anden tries to speak to the people rioting in the streets. Day must leave the weak June behind in order to save the Elector. He climbs up to a 10th- floor balcony and rallies the people to support Anden.
In separate hospital rooms, June recovers from her illness and is tested to make sure the Colonies haven't planted any weapons in her body or brain. The same tests are run on Day, while he waits to see his brother, Eden. June is given the all-clear sign, and Anden arrives. He asks her to consider training to be the Princeps, the second most powerful person in the Republic. The position is one that will require her to be by Anden's side for the next 10 years. It is also a position that often leads to marriage with the Elector.
Anden asks her to consider his proposal. Day is reunited with his brother, who is now blind from the plague. A doctor pulls Day to another room and reveals that experiments performed on him when he was younger are now having dire consequences. Day has an inoperable brain tumor.
He puts off seeing June until the following day, and he doesn't tell her about his imminent death. Instead, he encourages her to train for the Princeps position. They share a passionate kiss goodbye with June believing Day is leaving her because of her past work with the Republic, which he can't forget.