Dink Meeker, one of the toon commanders in Rat Army had requested Ender. He trains Ender and makes him a part of the toon. After practice one day though, Ender stays back and watches Dink, who floats about in zero gravity for awhile. He tells Ender that it is prevent himself from going crazy, which Battle School can do to children; they are not like the children back home. Dink does not even think the bugger war is real, but rather a ploy to keep things on Earth united. While Ender does not believe him, it does make him question things more. His additional practices with the Launchies continue but some of the older boys begin picking on them. When it turns into a fight in zero gravity, the other Launchies are able to escape and Ender fights his way out. The teachers do nothing in response but the other commanders send some of their soldiers to protect them during practice and encourage Ender to continue. Aside from that fight, Ender also becomes disturbed at the fantasy game, which shows him a picture of Peter when he looks in the mirror.

Back on Earth, the actual Peter seems to be doing better, enjoying school and getting along with others, since the family moved. Valentine knows better, having seen squirrel body in the woods that Peter had pinned and watched while it died. He has also been using his spare time to monitor Russian troop movements and is convinced that the Earth will go to war once the bugger threat is gone. He wants Valentine to help him come up with identities on the nets so that they can write to influence the public mind and be taken seriously, since then no one would know they are children. In this way, he can prevent the war from escalating. He even admits to his own fear of becoming as cruel and evil as Valentine thinks he is, and, while she is not sure if he means it or not, she is sure that she is more powerful than him, so she agrees. They take on the identities of Locke and Demosthenes, and each writes the column that is in opposition to their actual views. The columns gradually gain in popularity.

Ender is unhappy at Battle School, because he has respect but not friendship, and feels despair when he cannot beat the fantasy game. Colonel Graff therefore talks to Valentine, asking for her help in making Ender happy again. He wants her to write a letter, and this one will be given to Ender, unlike all the previous ones she had written. Although she is hesitant, she does so. When Ender gets it, he cries because it means that even his memory of Valentine has been destroyed. He returns to the fantasy game, in which the snake turns into Valentine, and he walks out of the tower room with her. Graff is pleased with Ender's mental recovery but Valentine is upset over selling out her brother.

Ender is put in charge of his own army, a new one called Dragon Army, with mostly untrained soldiers. Ender is determined to make them good, but in doing so, soon finds himself treating his best soldier, Bean, the same way Graff had treated him. Along with other new rules, Ender is also no longer able to practice with his old Launchie friends and now things between himself and Alai are more distant as they have become competitors.

Dragon Army is put into an early and rigorous series of battles, all of which they win, which does not help maintain Ender's previous friendships. He begins watching old videos of the bugger wars in order to learn from their techniques. He also asks Bean to create a small group and have them try out everything Bean can think of, even if it seems stupid. One of the things they discover is that by using a thin wire, they are able to change directions quickly in midair, a technique that they are able to use in battle.

Returning from practice, Ender notices a number of boys in the halls acting suspicious. Petra and Dink both warn him that he is in danger; Bonzo has a grudge against him and intends to hurt him. Ender does not think too much about it, trusting the teachers to keep him safe. Meanwhile, Dragon Army keeps winning battles, having become a united and skilled army. Tired after yet another battle, Ender goes to the gym and starts to shower, not realizing that he is alone. Bonzo and a group of other boys corner him in the shower, but, once again, Ender is able to talk Bonzo into a one-on-one fight. Dink arrives and tries to prevent the fight but the other boys hold him back.

Ender and Bonzo fight, until Ender is able to bring his head up into Bonzo's face and then kick him in the crotch. Bonzo falls (dead), and while the medical staff and his friends rush in, Dink leads Ender away. Ender now realizes that no one will ever come to his aid, and then he cries because he did not want to hurt Bonzo. He is so upset over the fight that when his army is given instructions later that day to fight against two armies at once, he sends his soldiers over to the gate to perform the victory ceremony without bothering to fight. He thus wins, but no longer cares about the game. As he lays in his room, Bean comes to tell him that the leaders of the Dragon Army have all been given positions in other armies. Ender soon receives news of his own advancement; he has graduated and will be sent to Command School.

Before going to Command School, Graff and Ender spend some time at a lakefront house in North Carolina where Ender can relax. Graff brings Valentine out to see him in hopes that she can help with Ender's mental recovery. Ender tells her that he is tired of the manipulation and does not want to kill anymore because in the moment he defeats an enemy, he loves them. Valentine, however, tells him that she is concerned about herself, and she wants Ender to protect her from the buggers as she used to protect him from Peter. Ender decides to return, having now also learned to love Earth. On the trip out to Command School, he talks with Graff about the buggers, of which little is known, but both agree that they want to be the ones to survive.

Command School is on a former bugger world, Eros, and its design makes Ender uncomfortable. He is given a teacher-Mazer Rackham, the commander who had been victorious against the buggers in a previous war. He shows Ender more of the bugger way of fighting, as well as about Dr. Device, a weapon that destabilizes things to the size of dirt particles. Instead of the Battle Room, Ender runs through scenarios on a simulator. As he becomes more skilled, squadron leaders (which turn out to be his friends from Battle School) are added, whom he can communicate with. Although he is not allowed to ever see them, he learns their strengths and weaknesses, and how to command them. The pressure builds, with increasingly more difficult battles, causing Ender to have restless nights, pass out during practice, and eat little.

Finally he is told it is his last day, with the battle being his final examination. The screen shows a bugger force that completely outnumbers his human fleet. Ender then stops caring about the rules and sees a way out, to prevent himself from becoming a commander. He maneuvers so that he can use the device on the planet, completely destroying it and wiping out the bugger fleet. Although he expects to be reprimanded for this action, the adults around him are instead cheering. Mazer Rackham explains to him that since he got to Command School, the battles had been real, and now the buggers are gone. Ender leaves the room and sleeps, furious at having been tricked into being a killer.

He sleeps through the fighting on Earth, which is ended by a Locke Proposal, put forth by Peter. When he does awake, he sees his friends, but one by one they return to Earth, and he does not. Graff becomes the new Minister of Colonization, ending the population limitation laws and sending out people to colonize former bugger colonies. This brings Valentine to Eros, where she tells Ender that she has made sure he can never return to Earth so that Peter will not be able to use him. Instead, she talks him into coming with her to the first new colony, with Ender serving as governor.

On that colony, Ender discovers a landscape built by the buggers to imitate the fantasy game. It is their way of communicating with him, in order to lead him to their still-surviving hive queen, who explains how the buggers regret the misunderstanding with the humans. Ender promises to find them a world where they can once again live. He also starts a kind of religion, as a Speaker for the Dead, telling the true story of the buggers, Peter, and others when they die.