While the Republic continues to war with the Colonies, June Iparis and Day Altan Wing ride in a cargo train into Las Vegas after escaping Day’s attempted execution. With a heavily injured leg, Day tries to stay upright on the streets while June watches for Patriots disguised as Republic soldiers and the announcement of the late Elector Primo’s death broadcasts overhead. When Day falls, the pair narrowly escapes arrest with the help of Kaede. She leads them to a Republic military apartment where they reunite with Tess and meet the Patriot leader, Razor, formally the Republic Commander Andrew DeSoto. They beg for his help to find Day’s brother, Eden, and pledge allegiance to the Patriots, who plan to kill the new Elector, Anden.

June helps Day bathe and the two kiss passionately. Day tells her he loves her, but she does not respond. June fights to earn trust from the Patriots while Day undergoes an advanced surgery to replace his injured leg. Razor puts an elaborate plan into motion in which June will lead Anden into a trap while Day reveals himself to the public and causes a revolution. Disguised as a soldier, Day boards a ship to Colorado with Kaede while June intentionally gets arrested by Thomas. Worried, Day leaves June behind while Thomas takes her to a Las Vegas penitentiary.

Day lands in Lamar, Colorado and Kaede leads Day to the Patriot base, repurposed from a series of tunnels below the city. He meets a group of other Patriots including Baxter and Pascao, two other Runners. He watches June over security footage and reconnects with Tess. Meanwhile, June convinces Thomas to take her to Denver, where she meets Anden. The two have dinner in an elaborate dining hall and she warns him of a false assassination plan. He asks for her trust and tells her that he wants to change the Republic for the better. She takes a lie detection test and, despite lying about the true assassination plan, passes. She struggles to remain loyal to the Patriots and questions her own intentions. Anden tells her that he is going to free Eden and eliminate the Trials, and she signals to Day to stop the assassination plan.

Day struggles to reform his relationship with a jealous Tess, who among other Patriots distrusts June. He sees June’s signal on the security footage and wonders what it means while he and the other Runners leave the base to bomb a railcar and steal supplies. The raid goes according to plan until Day finds a train car marked with an “X”, designating plague experiments and likely a relationship to Eden. Inside the car, Day finds a young boy in a glass cage who reports that he is being used as a biological weapon on the warfront. Civilians and soldiers recognize Day, and rumors that he is alive spread through the Republic. Convinced the bombing was an attempt on his life, Anden reroutes his planned speaking tour from Lamar to Pierra, Colorado

June begins to feel sick before she arrives at the courthouse where the Elector will pardon her for helping Day escape execution. She instructs the Elector to follow her instructions without question, and then pretends to faint in the courtroom. Anden instructs her guards to take them both to the hospital, but Razor, acting as Commander DeSoto, instructs them to continue towards Pierra as planned. The Patriots make their move, but Day deviates from the plan and saves the Elector. He and June run to the Patriot base, accompanied by Tess, who refuses to enter. Day and June seal off the tunnel entrance with an explosion and she tells him about Anden’s desire to change. Feeling betrayed, Day yells at her and tells her that Anden cannot be trusted. She gets increasingly sick, and Day takes care of her until they realize someone is coming down the tunnel for them. He picks her up and they walk through the rest of the tunnel.

The pair emerge in the Colonies city of Tribune, and they marvel at the pervasive advertisements and corporate influence. They are soon caught and taken to a hospital. The guards recognize Day and crowds of excited Colonies citizens gather outside the building. Day spots Kaede in the crowd with a sign warning him to go back to the Republic, and throws rocks at his window until he comes outside. She shows him the dark side of Tribune, where homeless and poor people are harassed and arrested by privatized police. She tells him that Razor was hired by the Republic Senate to kill Anden because he was too progressive, and Day sees Eden’s release on a newsreel. They decide to go back.

While Day talks with Kaede, June talks to Metias in a dream. He guides her through the assassination attempt and she realizes that Razor is working for the Republic Senate. She wakes up to a group of Colonies soldiers, who recognize her as the Republic’s prodigy. Day and Kaede come back just in time to help her escape the guards, and the three of them head to the roof to steal a jet. Engulfed in gunfire, they take off from the roof. Kaede maneuvers the jet first away from Colonies jets, and then Republic defenses. They fly through a train tunnel in the Armor and land in the streets of Denver. Day runs through crowds of soldiers and rioters to the Capitol Tower, where Anden stands on a balcony, attempting to calm the rioters. Day climbs to the adjoining balcony and addresses the crowds. He tells the Senate to release arrested Patriots, and he asks the crowd to trust in Anden. The crowd responds in cheers.

Day and June are both taken to a hospital to be tested for Colonies mind control. Cleared of Colonies influence, June is discharged and Anden asks her to train as the next Senate Princeps. Day is reunited with Eden before speaking to his doctor, who tells him he has a brain tumor and will soon die. Two days later, he arrives at the apartment June now resides in, paid for by the Republic. He gives her a ruby pendant and tells her to accept Anden’s offer. Realizing the implications of his words, she asks if they can find a way to be together. He tells her that too much has happened, but does not tell her he is sick. He turns to leave but she calls out to him. He turns and kisses her, then walks out the door.