The war is over, won by Ender Wiggin and his team of brilliant child-warriors. The enemy is destroyed, the human race is saved. Ender himself cannot return to the planet, but his crew has gone home to their families, scattered across the globe. The Battle School is no more.
But with the external threat gone, the Earth has become a battlefield once more. The children of Battle School are more than heroes; they are potential weapons that can bring power to the countries that control them. One by one, all of Ender's Jeesh is kidnapped. Only Bean escapes; and he turns for help to Ender's brother Peter.
Peter Wiggin, Ender's older brother, has already been manipulating the politics of Earth from behind the scenes. With Bean's help, he will eventually rule the world.
Shadow of the Hegemon goes into much more detail with the character Bean as he goes into hiding with a nun named Sister Carlotta, who is like a mother to him, when a Battle School expulsée tries to assassinate him. After some analyses, Bean begins to suspect the mysterious figure trying to end his life is Achilles, a child from the streets of Rotterdam, who also has it out for Bean after Bean made Achilles confess all of the murders he has committed, getting him kicked out of Battle School. And Bean's analyses, as always, is correct. From the viewpoint of the kidnapped Petra Arkanian, we find out Achilles has been manipulating his way through Russia's intelligence service and has obtained a position where he can get whatever he wants. Bean collaborates with Locke (Peter Wiggin) to get Achilles kicked out of Russia after Bean receives the location of Achilles' whereabouts from a coded message from Petra. After his removal from Russia, Achilles is promptly taken in by the Indian government where again, he has a position of power. Bean eventually makes it to Thailand where he is greeted by another Battle School graduate, Suriyawong. After much betrayal, including one by the Thai military Commander-in-Chief, Sister Carlotta is killed by a Chinese SAM while in an airplane en route to Thailand. Unfortunately, Achilles is able to get away.