Day and his brother, Eden, have been moved to San Francisco where both are receiving medical treatment. Eden is recovering from a government-created plague that has left him mostly blind. Day, once the symbol of revolution for the people of the Republic, is dying of a brain tumor. Republic doctors are medicating him to prepare him for the removal of the tumor, but his condition is worsening.
June has been training for the role of Princeps since she and Day parted almost a year earlier. The Princeps is the second-in-command of the government, supporting its head, the Elector. Elector Anden orders June to invite Day to a special banquet.
The Colonies and the Republic have been at war for generations. Anden has negotiated a temporary peace, but the Colonies demand that they be given the antidote for the plague that the Republic loosed on them or they will again declare war. The only way to get the cure is by running experiments on Eden's blood. June is the only person who may convince Day to let Eden be studied, but even she is unable to convince Day to agree to the plan.
Day's condition worsens, and he is rushed to the hospital with a debilitating headache. The doctors warn him that he has less than two months to live. They hope a new medical protocol will make it possible for them to operate, but it may not work in time. He is told to prepare for the worst.
News of Day's illness leaks out to the press, and June sees the report on a Jumbotron. She immediately seeks him out at his apartment. As he's feeling better, they leave Eden with his caretaker and go out for dinner. While out, the Colonies attack. June, Day, and Eden are evacuated to an exclusive underground bunker kept for the elite of the Republic. June and Day convince the Elector to evacuate the poorer sectors to the wealthy neighborhoods in the center of the city for their protection, as the attack seems to be on the edges of the capital. Along the way, news arrives that several prisoners have escaped, including Commander Jameson and Thomas, the family friend who killed June's brother. June knows it isn't a coincidence that Commander Jameson escaped on the same day the Colonies attacked.
Once inside the bunker, they discover that several of their former colleagues from the rebel group known as the Patriots are being held prisoner. Included in the group is Tess, Day's former best friend. They learn that Tess, Pascao and several others had escaped to Canada but returned when they heard Day was ill.
Anden orders their shackles removed, but they are to remain guarded while they are evacuated to Los Angeles. Later, he tells Day and June that the Colonies have enlisted aid from Africa. With the added military help, they will easily defeat the Republic. Anden and June will travel to Antarctica to plea for their assistance to defeat the Colonies. Day convinces the Elector to let him lead the remaining Patriots in a guerilla war against the Colonies.
The meeting with the president of Antarctica does not go well. The ruler of Antarctica insists that Anden give up Republic land to gain his country's support and ability to find a cure for the plague. Until then, the United Nations will seal up the Republic's ports and borders to contain the disease.
Later, unable to sleep, June wanders the hallways. After watching informational holograms about Day and the former United States of America, she bumps into Anden, who is also unable to sleep. He invites her to his room where they share some wine. He opens up to her about his inner conflict about being Elector.
He kisses her. She is moved by his vulnerability and his passion, but she will not betray her feelings for Day. Before they return to the Republic, they learn that Denver, the capital, has fallen to the Colonies.
Day and the Patriots sabotage the Colonial air strip, blowing up several of their airships. As they are chased by soldiers, Thomas appears. He draws a weapon and shoots the Colonial soldiers, allowing Day and the others to escape. Thomas is killed. The excitement and explosions bring on another of Day's headaches, and he falls unconscious. He is brought to a hospital in Los Angeles.
While he recovers, the Chancellor of the Colonies secretly contacts him. The Chancellor wants Day to defect to the Colonies and persuade the rest of the Republic to surrender peacefully. In exchange, the Colonies will care for Eden, June, and the Patriots. If Day refuses, June will be executed when the Colonies defeat the Republic. As Day contemplates what he will do, he finds that Tess is also in the hospital and has been infected with the plague.
June arrives in Los Angeles. Day visits her in her quarters and tells her of his contact with the Chancellor. The two admit their love for one another and share a romantic encounter.
Later, Day wakes from a nightmare. He sneaks away from June's apartment and finds his old house. He weeps at the kitchen table for everything he has lost because of his involvement with her. June has secretly followed him. She knows that because of her, his mother and older brother were killed.
Eden agrees to let the doctors experiment on him in order to find a cure for the plague. While keeping his brother company at the hospital, Day comes up with a plan to defeat the Colonies. He and the Patriots will rally the common people to fight. Day will pretend to work with the Chancellor, but then call for the people to rebel. June barely escapes an assassination attempt by Commander Jameson.
Anden is sure Jameson is working to coordinate the Colonies' next attack in Los Angeles. That night, he asks if June is sure she wants to continue training for the Princeps position. She admits that she's a soldier, not a politician. She resigns, leaving Anden to face the upcoming revolution without her by his side.
Day and Pascao plaster Los Angeles with graffiti rallying the people to wait for Day's message. When he returns to visit Eden, he talks with one of the lab technicians. Day learns that the virulent strain of plague now spreading did not come from Eden. His strain was mutated by the Colonies, but the original carrier is unknown. Without that person, the doctors will not be able to find a cure.
The following day, Colonial and African airships hover over Los Angeles. Anden officially surrenders to the Chancellor. As June and Day discuss their next attack, Day also explains that Eden cannot help find the plague's cure. After discussing the problem with the lab technician, June realizes that she may be the new plague's patient zero. When she and Day escaped to the Colonies the previous year, she was treated in one of their hospitals.
While June is being tested, Day arranges to make a deal with the Chancellor. June's blood holds enough of the plague that the doctors can develop an antidote. They give it to Tess and hope it cures her. Colony soldiers arrive at the hospital and attempt to take June prisoner. She fights back and is ultimately saved by Tess, who has rapidly recovered from her illness.
Day meets with the Chancellor on his airship. He convinces the Chancellor that he is ready to make an announcement giving his support to the Colonies, but as the speech is broadcast live, Day calls the people to fight for the Republic. He barely manages to escape capture from the Colonies' guards.
Day heads off to rendezvous with June and Eden. June helps Eden and his nurse leave the hospital. She climbs to a nearby roof in order to try and draw fire away from Eden as the nurse waits for help. The nurse panics as shots explode around her, and she abandons Eden. Day arrives to help his brother but is soon shot himself. June recognizes Commander Jameson as the sniper and sets off to stop Commander Jameson.
June shoots and misses her target. Commander Jameson fires but also misses. The two fight hand to hand, trading blows until June manages to send Jameson tumbling over the roof. Jameson grabs onto June's arm, dislocating it and using it to hang on. June screams for Republic soldiers to shoot the commander, which they do. Jameson falls to her death.
Day has been shot several times. He is barely hanging on to life when June reaches his side. They declare their love for each other as Day slips into unconsciousness. Doctors operate on the wounds and decide his brain can't wait for the full course of medicine they'd like before they operate on his tumor. They remove it, and Day falls into a coma for five months.
During that time, Antarctica defends the Republic, and peace is restored to the world. June, Tess and Eden stay by Day's side throughout the long months. When he finally regains consciousness, he is fully healed, except that he cannot remember the past year of his life. Without those memories, he has no tie to June and no feelings for her, good or bad. June realizes that if she doesn't stay in his life, he won't remember the deaths of his mother and older brother either. She decides to sacrifice her love for him and walk away from their relationship so that he can completely heal.
An epilogue tells about the 10 years following Day's awakening. He and Eden are given a home in Antarctica where Eden became a successful engineer and Day is recruited by the intelligence service. June remains in the military, eventually becoming the youngest commander in Republic history.
She and Anden date for several years, but by the time she is 26, she realizes she can never love Anden the way he deserves. They break up but remain good friends, and June fiercely protects him as her government's leader.
The epilogue ends on her 28th birthday. June plans to celebrate it with Tess and Pascao. She stayed in touch with both over the years. On her way to dinner, June sees Eden and Day on the street. She learns they have arrived in the city so Eden can interview for a job. June passes them without acknowledging them, even though Eden recognizes her.
A few moments later, Day follows her. He asks if they know each other. June lies and tells him no. As Day continues to study her face, he insists that he does know her. He just can't remember how, but he knows he's been searching for her for a long time. In the end, he takes her hand and introduces himself to her, reminiscent of his dream long ago when he'd wished they could have met as strangers instead of as a soldier and a rebel.