This post contains spoilers!
This story takes place in the Republic (which long ago was known as the western coast of the United States). There are various sectors within the Republic - most of which are poor, dirty slums. The Republic is at war with it's neighbors, the Colonies.
In the Republic, kids are forced to take a test known as the trials. If their score is high, they are assigned to a top university where they undergo highly specialized training which will allow them to eventually serve the Republic. If their score is low, they are immediately sent away to labor camps, never to see their families again.
June (15) is from an elite family of the Republic. Her parents are dead and she lives with her older brother, Metias, in a nice, affluent area of the Republic. Metias is a captain with the Republic forces. June, is just about to complete her training to follow in her brother's footsteps. She is something of a military prodigy - the only one to achieve a perfect score in the trials.
Day (15) is from the slums of the Republic's Lake Sector. After failing his trial (we later learn the Republic lied about his trials - he didn't really fail, he actually got a perfect score), he is sent away from his family. Day lives on the streets and over the years commits acts of sabotage and crimes against the Republic. Because of this, he has become the Republic's most wanted criminal. However, no one knows for sure his true identity and he eludes capture. While living on the streets, Day has partnered up with a younger girl, Tess. She is an orphan that he encountered and took under his wings. Day's family consists of his mom, older brother, John, and younger brother, Eden. His father is dead. Day's family presumes him to be dead as well. Only John knows the truth - that Day is alive. They keep the truth from their mother and younger brother because it would be too risky for them if Day were ever captured by the Republic. Day secretly tries to help out his poor family by bringing them food and supplies that he scavenges from the streets.
Thomas - A soldier; originally from the poor sector but worked his way up through the ranks and is 2nd in command under Metias; long-time friend of Metias; seems to harbor secret affection for June.
Commander Jameson - Ruthless superior of Metias; when Metias is killed, she allows June to serve in her unit.
Kaede - A tough girl bartender; she faces off in the Skiz fight with June; we later learn that she is a Patriot rebel
Viruses rage within the poor sectors of the Republic. The army (plague patrol) routinely performs door-to-door sweeps to tests the household members for the virus. Those found to be infected are quarantined to their homes and basically left to die. A large X is marked on the home to indicate the presence of the virus. During one of the sweeps, Day witnesses the soldiers mark his mother's house with a special X and soon discovers that his little brother, Eden, has become infected. Day is determined to somehow get his hands on "the cures" - whether he has to buy them or steal them.
In a botched attempt at breaking in to a Republic lab to steal the cures, Day is almost apprehended. While making a quick getaway, he comes face-to-face with soldier Metias but manages to escape. When Metias is found dead at the scene, Day is blamed for the murder. Filled with anger, June vows to capture Day and make him pay for the death of her brother.
June is allowed to graduate early and go to work for the Republic. For her first mission, she plans an undercover operation to try and find Day. She spends several days out on the streets, living among the poor, scouring for information that could lead to Day. When she inadvertently becomes involved in a Skiz fight, June finds herself injured and in a dangerous situation. The crowd wants her to stay and continue fighting but June refuses and walks away. The angry and unruly crowd tries to come after her but a mysterious boy suddenly appears at her side and helps her escape. June finds the boy attractive and is drawn to him. They do not exchange names or information - it's too difficult to trust anyone on the streets - and spend several days together. He, along with a young girl, help June as she heals from her wound. It's only a matter of time before June realizes that the boy is Day. She is conflicted because even though she knows he is the enemy, she is still feeling a connection to him.
June informs Thomas of her findings and exposes Day and his family. During the raid on Day's home, Thomas kills Day's mother (on orders from Commander Jameson). Day and his brothers are captured and taken away by the Republic. While imprisoned, Day doesn't know what has become of his brothers. He soon learns his own fate when he is sentenced to die in a few short days. Crowds from the slum sectors show up in protests, causing near riots over the upcoming execution.
Meanwhile, June continues to feel a connection to Day. Although Day insists he did not kill Metias, she is not sure if she can believe him. She is shocked when Day tells her that he thinks the Republic controls the virus - who gets it and when. He also tells her the truth about the so-called labor camps. The children who fail their trials are not really sent away to labor camps...they are used for medical experiments and/or killed by the Republic. He tells her that when he failed his own trials, the Republic took him away and experimented on him. Only when they thought he had died, was he able to escape to the streets. For appearances, June remains loyal to the Republic. But, she secretly starts investigating on her own. She studies the crime scene photos taken when Metias died. She pours through her brother's journals and discovers some cryptic hidden messages. This leads her to a secret website, made by Metias, to reveal the truth about the Republic to June. Everything Day had told her is true. Thomas is the true killer of Metias. Furthermore, she learns that her parents were killed after learning the truth about the Republic's involvement with the virus.
June devises a plan to help Day and John escape and intends to carry it out just before his execution. She reaches out to Tess and Kaede, hoping that the Patriots will be able to assist in freeing Day. Commander Jameson throws the plan off somewhat when she suddenly moves up Day's execution day. Kaede and the Patriots show up to help. But, while June is trying to flee with Day and John, it becomes clear they are not going to be able to pull of the escape. In a split second decision, John sacrifices himself so that June and Day can get away. The Republic executes John, telling the public that it was Day who was put to death. With the help of the Patriots, June and Day escape to Barstow, California. It's a sector that's far enough away for them to hide out for awhile and decide their next move.
Day tells June that he wants to head for Vegas. This is where he hopes to find Tess and make sure that she is safe with the Patriots. He also intends to head back and find out what happened to his younger brother, Eden. He tells June that it's okay if she doesn't want to stay with him but she pledges to stay and join him in his mission.