Several things happen after Ender destroys the bugger world. First, he finds out that he was not involved in a simulation at all. He was fighting a real war against the buggers. Because of him, the humans won the war.

As Graff explains to Ender, he had to be tricked into thinking the war was a game. To win, the humans needed someone like Ender, a child who could think and react quickly, learn to completely empathize with and understand the buggers, and also put his whole heart into winning against them. If he had known that they were real, his empathy and compassion towards them would have stopped him from taking the final step that destroyed them all.

Ender is not happy to have been used to commit genocide against another species. However, he later finds the pupa of the bugger's queen. She is able to communicate with him through thoughts and can also impress her emotions on him. She tells him how he can take care of her cocoon so that when the time is right, she can start a new colony of buggers with ten thousand children. She also tells him that the buggers would never have fought with the humans if they had thought they were sentient beings:

We are like you; the thought pressed into his mind. We did not mean to murder, and when we understood, we never came again. We thought we were the only thinking beings in the universe.

Ender decides to travel with her to find a home where she can thrive.