On Opposite Sides
In the beginning we get an introduction to the two main characters and where their lives are. Day is a street criminal who is on the run from the Republic; he scavenges in the trash for food, steals from the Republic, and came from one of the poorest sectors of Los Angeles. June, on the other hand, is a prodigy from a respected military family. She's graduating from college early and lives in a big, nice apartment with her brother, who's a captain in the military. They come from such different areas that it seems like it'd be impossible for their lives to intersect… right?
Cat and Mouse
Things get complicated when Captain Metias (June's big bro) is killed while patrolling the hospital one night. The government tells June that Day did it, so she sets off to hunt him down and bring him to justice. As June hunts for a boy that she doesn't know, and Day runs from a government agent that he doesn't know, their paths intersect and they start to form a friendship. Of course, June eventually finds out that the boy she's been spending so much time with (and enjoying kissing) is actually the criminal Day, and she has to make a difficult decision.
The climax of the story happens when June discovers Day's identity and calls in the government to come collect him as he's trying to protect his family. Things do not go as planned—Captain Jameson orders Thomas to kill Day's mother and they take both John and Eden (Day's brothers) into custody. The whole event is very dramatic and sad, and ends with Day injured, devastated, and in prison, while June starts to feel ambivalent about her part in the Republic's master plan.
The Truth Comes Out
June begins to uncover some disturbing truths through Metias's diaries. She finds out that her parents were killed by the government, and that Day didn't kill her brother—Thomas did. Due to these discoveries, June decides to turn her back on the government that she's been such a loyal citizen to this whole time and help Day escape. As soon as this choice is made, she starts planning, letting Day know, and enlisting the help of Kaede and the other Patriots.
No Turning Back
Once the plan is in place, June has to go through with it. When she gets the chance, she breaks out with Day and they rush past all the guards with the help of the Patriots. They pick up John—Day's lookalike brother—but at the last minute he pretends to be Day in order to buy them some time to escape. After this happens, there's no turning back for any of them. John has chosen his death, Day is making his way to freedom, and June has committed to living out the rest of her life as a traitor to the Republic.