Admiral Chamrajnagar welcomes Colonel Graff to I.F. command by questioning the three month vacation that he let Ender take. Graff points out that it was necessary for Ender to be ready. Chamrajnagar tells Graff of their plans for Ender, and Graff says he is only there to help the boy. They dislike each other, but respect each other, and both know that Ender is the only one who matters. Ender spends his time alone or with Graff, occasionally taking classes but mostly working with the simulator. In this game Ender starts commanding a single fighter but soon is in charge of an entire fleet. After a year Ender finds it easy, and he says so to Graff.
The next day Mazer Rackham introduces himself to Ender by attacking him and subduing him, explaining to the boy that he will be his teacher because he will be his enemy. Rackham has a brilliant mind, and Ender respects that. Rackham explains how he took a relativistic trip in order to be alive to train the commander of the Third Invasion. Together they watch tapes of the First and Second Invasions. Rackham explains why the buggers stopped fighting after he attacked a single ship—he destroyed the queen ship. The enemy is like highly evolved insects, and they do not think to each other but are more like many parts of a single organism, with all thought coming from the queen. Rackham explains modern weapons to Ender as well as the one advantage humans have over buggers: every pilot is a thinking being, and so people can carry out many more strategies at once than the buggers.
Ender is moved into a new simulator where he is to command an entire fleet, this time with three-dozen real squadron leaders made up of all his best friends and opponents from Battle School. Rackham tells him that he is preparing more and more complex simulations and that Ender cannot quit because winning is everything. Ender spends hours practicing with his squad leaders and battles are fought every couple of days. Afterwards he and Mazer go over them to see what he could have done differently. Ender is lonely and tired, but he does not stop. He is a commander, not a friend, to his leaders. Ender dreams strange dreams about the buggers and he has difficulty sleeping. He breaks down physically once, and he wakes up in time to win a battle and go back to sleep. He fights when awake and then sleeps, and the days blend together. Then one day Mazer tells him that the battle will be his final examination in Command School. Ender is happy to hear that because he is tired of it all. Then he sees the battle, and he despairs, for he is vastly outnumbered. He does not even want to play but decides that he will win an unfair battle rather than be beaten unfairly. Ender wins the battle by destroying the planet that the enemy lived on, and the room explodes in cheers. Rackham tells him that he has actually been the fleet commander of the Third Invasion and that he just destroyed the buggers completely. Ender is angry with Rackham and Graff for using him. He did not want to hurt anyone and now has destroyed an entire race without his knowledge. Ender sleeps through the five days of war on earth and when he awakens, the Locke Proposal (put forth by Peter to settle the war) has been accepted and all of his friends are there to tell him what he has missed.
After Ender has won the final battle, assuring humanity's safety from the Buggers, Ender is the only one who does not celebrate. He feels only sadness and anger. He is sad because he destroyed the buggers, and he did not want to hurt anyone. He is angry because he was manipulated perfectly, and Graff and Rackham got everything out of him that they wanted. Ender is really the only character who feels for the buggers, for he is the only one whose compassion extends not just to all human beings, but to all sentient beings. The buggers are intelligent life, and to kill them all is a horrible thing to Ender, even if there was no choice. Ender is angry because he still feels he should have had a choice. He knows, however, that the adults did what they had to do to save their species, and that whatever price he has to pay would be worth it to them. Graff and Rackham know that Ender feels betrayed, and the only justification they can offer is that they had no choice. Their manipulation was wrong, but it was the right thing to do for the survival of humanity. Ender Wiggin is a genius, and he understands people's motivations, but he is also tired of being used to fight other people's wars. Ender does not hate the buggers, and so this was not a war he would have consciously fought. At the same time, Graff, Rackham and the I.F. leaders knew that, and that is why they had to make it seem like a game.
Throughout the book, Ender has been a part of games, and the end of the novel blurs the distinction between game and reality. In Battle School and in Command School the games have real meaning because the games change lives. A continual theme throughout Card's novel is that games do not exist in opposition to reality. Card suggests that every action we take has meaning. We may not understand the meaning, and others may be manipulating the actions, but the meaning exists nonetheless. Moreover, the way that Ender wins all of the big games is by breaking the rules. Time and time again he is put in a situation where the only way out is to play the game a way it is not played. If games are reality and the rules of games must be broken, then it seems that there are no rules that cannot be broken. This is precisely the philosophy that Rackham and Graff believe justifies their use of Ender and his friends, but Ender is the only one of the children who fully understands the philosophy's implications. It means that mankind really had a right to destroy the buggers. And Ender is the only one who disagrees. He thinks there should have been a way to save mankind without war, and if left to himself he would avoid conflict. It is only when placed in certain situations that war is necessary. In those circumstances Ender always wins, but he wishes not to have to face them altogether. This does not demonstrate Ender's cowardice, but rather his nobility. He would always be willing to take the more difficult road and try to find a way to circumvent war. Again and again Ender has triumphed over impossible odds by coming up with a brilliant solution that breaks the rules of the game, but in doing so, his anger was always directed at the game itself. Unlike Peter, who finds pleasure in playing games, Ender never hated a single one of the people, armies, or buggers he fought, and it is the games that he wishes to stop playing.