The Republic of America and its long-time enemy, the Colonies, are on the eve of drafting a peace treaty under the leadership of the Republic’s new Elector Primo, Anden Stavropolous. Day Alton Wing walks through a futuristic San Francisco, the city in the Republic in which he lives with his brother Eden. He battles a headache, caused by a terminal brain tumor, with hallucinogenic medication and envisions Tess, a close friend, and June Iparis, the Republic soldier and now Princeps-Elect that saved him from execution. He explores the San Francisco nightlife in disguise, attempting to avoid the celebrity he has gained as a political hero for the people. He is kissing a girl in an alley when June contacts him over the permanent earpiece Day wears. Day is surprised, as they have not spoken in eight months, and even more surprised when June asks him to come to Denver, the capitol city, for an emergency meeting. She tells him that the Colonies, what used to be the eastern United States, has discovered a plague outbreak that they have traced back to the Republic and believe it is an act of war.

Day lands in Denver and a senator’s daughter takes him shopping. Meanwhile, June watches the trials of Commander Jameson and Thomas Bryant, two traitorous Republic soldiers who assassinated June’s brother Metias and attempted to assassinate Anden. They are sentenced to death. June and Day meet at a government banquet later that evening and quickly enter a conference room with Anden and the two other Princeps-Elects, Serge Carmichael and Mariana Dupree. Anden tells Day that the plague in the Colonies likely accidentally came from Eden, who was previously used by the Republic for experimentation and biological warfare. He asks Day to allow the Republic to experiment on Eden once more to find a cure and prevent invasion by the Colonies. Day refuses.

Later that night, Day wakes up from a nightmare with an excruciating headache. Eden and their caretaker Lucy try to comfort him and decide to call an ambulance. The medics take Day to the hospital and run tests while Day comes in and out of consciousness. When he wakes up, the doctors tell him that he has only a few months to live. Unaware of Day’s situation, June goes to see Thomas in his cell before his execution. Commander Jameson gets her attention from her cell first and warns June that they are the same. Shaken, June continues to see Thomas. Thomas tells her the full story of Metias’s death – the two were close friends and nearly lovers, but Commander Jameson ordered Thomas to kill Metias and he felt he had no choice but to comply. After the conversation, June goes for a run to clear her head. She talks with Anden on the track and sees a headline on a JumboTron that announces Day has been admitted to the hospital.

June goes to visit Day and they go to a small café for lunch. He tells her that he has a brain tumor and will likely not survive more than two months. An air raid siren goes off during their conversation, indicating that the Colonies are invading the city. Day and June evacuate with Eden and Anden to an underground bunker where a series of subway trains take citizens out of the city as Colonies ships bomb the city. Day is angered to learn that poor parts of the city do not have bunkers, and refuses to leave until he is assured that the poor will be given access to the wealthy sector bunkers. June learns that Commander Jameson and Thomas have escaped during the bombing, and Eden tells Day that he wants to give himself to the Republic to find a cure. As June, Anden, Eden, Lucy and Day walk towards the evacuation train, Day and June see Tess being held as a prisoner in a nearby room with a few other Patriots – members of an underground resistance that fights for unification of the Colonies and Republic. Day demands their release, and they agree to go above ground to fight against the Colonies.

June, Anden, and the two Princeps-Elects fly to Ross City, Antarctica to ask for aid. June is awed by the Antarctican technology, which assigns every citizen points for performing good deeds. The Antarcticans refuse to aid the Republic unless they give up territory. June and Anden discuss the role of emotion in politics and reminisce about their families, who are both deceased. Meanwhile, Day reconnects with Tess and prepares to attack the Colonies invaders. He and the Patriots place bombs on the landed Colonies ships and disable their weapons. He and Pascao, another Patriot Runner, narrowly escape the soldiers’ retaliation as Thomas sacrifices himself to save them. Once safe, Day collapses from another headache.

Day wakes up in a hospital in Los Angeles. He receives a secret call from the Chancellor of the Colonies who asks him to publicly surrender to the Colonies in exchange for Eden and June’s safety, and gives him three days to decide. June returns to Los Angeles and sees soldiers cooperating with citizens to find placement for the recent evacuees from Denver. The JumboTrons, which usually display Republic news and propaganda, suddenly display a message from the Colonies that encourages citizens to fight against the Republic in exchange for money. Anden takes June to the hospital where Day is waiting. He shows her an isolated room where Tess is being kept – she is infected with the mutant plague.

June and Day return to her apartment to talk. They express their love for each other and then sleep together. In the middle of the night, Day wakes up from a nightmare. He gets out of bed without disturbing June and leaves. He walks through the city back to the neighborhood where he grew up. He finds his old home and goes inside. He thinks about his brother John, mother, and father, who were all killed by Republic soldiers, and cries. Unbeknownst to him, June has woken up and follows him. She watches him and feels guilty for being part of the patrol that killed his mother.

The doctors and lab technicians at the hospital begin to experiment on Eden to find a cure and Day tries to comfort him. June sees Commander Jameson in disguise while she waits for a jeep to take her to a Senate meeting and follows her. Commander Jameson turns on her and nearly kills her before Republic soldiers come to June’s rescue. They take June to the hospital with Anden and Day tells them that he has a plan to defeat the Colonies. In the Senate meeting later that Day, June proposes a fake surrender to the Colonies to give them time to build forces and take their enemy by surprise. Day and Pascao mark doors throughout the city with “LISTEN FOR ME” and Colonies ships approach.

Back at the hospital, the lab techs tell Day and June that Eden’s blood cannot provide them with a complete cure to the plague. June realizes that she carries the missing element and offers herself for experimentation. Day contacts the Chancellor and agrees to surrender to him, then places bombs on the landing docks around the city with Pascao. Day broadcasts to the citizens that they need to fight against the Colonies, much to the surprise of the Chancellor, and the bombs begin to go off. The city erupts into a war zone and June starts to help evacuate the hospital. Day joins them and tries to evacuate Eden, but Commander Jameson begins shooting at him from a rooftop. June finds her and after a difficult hand-to-hand fight, throws her off the roof. June finds Day bleeding in the street below.

The narration jumps forward five months. The Colonies retreated and a peace treaty was drafted after Antarctica intervened, and Day has been in a coma since the attack on Los Angeles. June goes to the hospital one morning and the doctor tells her that he has woken up, but no longer remembers her. She decides to keep her identity a secret to prevent hurting him. Ten years later, Day and Eden visit Los Angeles. June sees them on the street and Day recognizes her. The two are re-introduced to each other.