A book that chronicles the 'lost years' between Ender's Game and Speaker for the Dead, Ender in Exile tells of Ender's initial set-off from Eros, the long journey to the first colony, Shakespeare, as well as his trip to the Indian-dominant colony of Ganges, where Ender encounters a familiar, yet not-so-familiar face. The court martial of Hyrum Graff is expanded upon; some light is shed on Graff's life after he was made Minister of Colonization, as well as where Mazer Rackham went off to after the Formic War.
Ender's journey starts out on Eros, after he defeated the Formics, and after Peter, under the alias of Locke, has quelled the warring nations into a temporary truce.
Valentine wishes to no longer be a part of Peter and his idea to rule the world. She tries to persuade her parents to come along with her to the ship in which Ender and several others would be traveling to the colony Shakespeare with, but they decline. Valentine goes alone to keep watch over Ender and be there as a maternal figure.
Meanwhile Alessandra and her mother, Dorabella, sign-up to go on to Shakespeare (a planet) in an attempt to get away from Dorabella's mother and money problems. They had planned to be put into stasis during the two year voyage, but several complications occurred and instead they remained awake, along with the crew, Ender, Valentine, Admiral Quincy Morgan (the captain), and some other colonists who opted against stasis.
Ender has a battle of wills throughout the voyage with Admiral Morgan, who attempts to usurp Ender's lawful position as Governor of Shakespeare, believing Ender to be a foolish child no one would follow. During the voyage, Dorabella seduces Admiral Morgan and tries to use her daughter, Alessandra, to seduce Ender hoping that, through her own marriage to Morgan and Alessandras' successful marrying of Ender, Morgan could rule Shakespeare using Ender as a puppet.
Upon arrival at Shakespeare, Ender quickly and easily crushes Morgan's attempted bloodless coup, with a little help from Minister of Colonization Hyrum Graff back on earth. Ender then successfully liberates Alessandra from her dominating mother, allowing her to finally live her life for herself. After two years as Governor, and completing 'The Hive Queen and the Hegemon', Ender convinces Valentine it's time for them to move on.
Ender's first stop, at the request of Hyrum Graff, is the Hindu colony of Ganges which is governed by Virlomi, a former battle school student who caused an uprising in India before she was subdued and exiled by Peter Wiggin's Hegemony. Once there, Ender agrees to help Virlomi quell an uprising by a group called 'The Natives of Ganges', which is led by an angry young man named Randall Firth under the delusion that he is the son of Achilles de Flandres. The so-called 'natives' have adopted 'The Hive Queen' as a rallying cry, and begun to turn the name of war hero Ender Wiggin into mud, coining the phrase 'Ender the Xenocide'.
Ender is able to peacefully neutralize Randall, nearly getting himself killed in the process. He reveals Randall's true parentage (two of Ender's old friends and squadron commanders, Julian 'Bean' Delphiki and Petra Arkanian Delphiki Wiggin), after which Randall renounces his secret name, Achilles, and renames himself Arkanian Delphiki. Shortly after, Ender reunites mother and son by ansible.
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