Ender has defeated the buggers, but he cannot return to Earth. Upon realizing this, his parents and sister (independently) work to manipulate Peter so that he (as Locke) will keep Ender in space forever. Valentine, however, chooses to join him in his exile. Ender ends up on a colony ship destined for Shakespeare colony (which Ender helps name) along with his sister Valentine, new characters Alessandra and her mother Isabella, and a bureaucratic captain whose intent it is to become governor of the colony upon his arrival. Ender, as the appointed governor, has different ideas. Through subtle maneuvering, Ender sets up a situation upon his arrival in which he immediately immerses himself and befriends all the soldiers he had commanded during the war. The captain is left without a choice but to submit to Ender as governor and return back to Earth with the ship. Isabella, who seduced and married the captain returns with her, but Alessandra decides to stay. Though she had fallen in love with Ender during the voyage, her choice is motivated by her desire to free herself from her domineering mother.

Meanwhile, Valentine completes a history of Battle School during the voyage and Ender learns that the lost Delphiki child is on route to Ganges colony, overseen by Virlomi. This child has the same genetic defect as Bean, and Graff asks that Ender head there after his time as governor in order to help Virlomi out (the child is manipulated into believing he is Achilles son by his surrogate mother, hence why Graff believes trouble will ultimately ensue).

While Ender is arriving on the planet, the xenobiologist Sel(and temporary governor after the original governor Vitaly passed away) goes on a trip investigating the area south of the original colony with Po, the son of an associate. On this trip they run across a species of hybrid buggers that were bred to mine gold and learn that they are able to communicate with them mentally.

As governor Ender succeeds masterfully in integrating the new colonists with the old, and establishing a thriving colony. He takes a particular interest in one boy (Abra), whom he takes on a journey to scout out a location for a new group of new colonists that will arrive shortly. Eventually they come across the bugger structures that were built to model what Ender saw in the fantasy game, and Ender finds the last queen in cocoon. Via a pre-chapter email we also learn that Ender meant for Abra to be given the cocoon in the event that Ender were to die. Upon finding the cocoon Ender also finally reopens the lines of communication with his parents.

Leaving Shakespeare, Ender and Valentine travel to Ganges where Ender confronts the lost Delphiki baby (who now calls himself Achille) with the truth of his parentage. The boy, who we learn was the originator of the Ender the Xenocide movement, beats Ender hoping to illicit the reaction that killed Bonzo and Stilson. Ender endures, however, and the boy, realizing the truth of what he has been told, takes the name Arkanian Delphiki. Ender introduces him to his mother via email.