Earth and its society have been changed irrevocably in the aftermath of Ender Wiggin's victory over the Formics. The unity forced upon the warring nations by an alien enemy has shattered. Nations are rising again, seeking territory and influence, and most of all, seeking to control the skills and loyalty of the children from the Battle School. But one person has a better idea. Peter Wiggin, Ender's older, more ruthless brother, sees that any hope for the future of Earth lies in restoring a sense of unity and purpose. And he has an irresistible call on the loyalty of Earth's young warriors. With Bean at his side, the two will reshape our future. Here is the continuing story of Bean and Petra, and the rest of Ender's Dragon Army, as they take their place in the new government of Earth.
Peter, Ender's brother, is now the Hegemon of Earth. Accepting a tip from inside China, where Achilles de Flandres is held prisoner, Peter had planned for Bean to operate the mission, but at the last minute (because he doubted Bean would cooperate) assigns Suriyawong, a Battle School student from Thailand, to rescue Achilles in transport, believing that he can spy on Achilles and then turn Achilles over to a country for trial.
Achilles is known to kill anyone who has seen him vulnerable. Bean and Petra, who also served under Ender and who is travelling with Bean, have both seen Achilles so and immediately go into hiding, preparing for a future confrontation. Bean believes Peter has seriously underestimated Achilles, and that he (Bean) is not safe unless he is hidden. During their travels, Petra convinces Bean to marry her and have children with her by taking him to Anton, the person who Anton's Key was named after. Bean is reluctant to have children, as he does not want his Anton's Key gene to be passed on. He finds Volescu, the original doctor who activated the key in his genes, and has him prepare nine embryos through artificial insemination. Volescu pretends to identify three embryos with Anton's Key and they are discarded. One of the remaining six is implanted into Petra, while the rest of them are placed under guard.
At the same time, a message is passed to Bean that Han Tzu, a comrade from Battle School, was not in fact the informant in the message sent to Peter about Achilles. Realizing that it had been a setup, Bean gets a message to Peter's parents, and they flee with Peter from the Hegemon's compound. Bean narrowly escapes an assassination attempt himself, and escapes to Damascus. There they find that another Battle School comrade, Alai, is the unrivaled Caliph of a nearly unified Muslim world. Meanwhile, their embryos are stolen, and Bean expects Achilles to use them to bait a trap for them.
Peter and his parents escape to the former Battle School, now rebranded Ellis Island, relying on the protection of Hyrum Graff, who is now Minister of Colonization. Shortly after they arrive, however, a message is sent betraying their presence. Faking their departure from the space station, Peter and his parents discover the traitor, one of the teachers at Battle School. The unmanned shuttle sent as a decoy is shot down over Brazil, the location of the former compound of the Hegemon, now occupied by Achilles.
In Shadow of the Hegemon, China had conquered India and Indochina. Alai plans to liberate them by invading first China, and then India once China has withdrawn its armies to defend the homeland. His invasion is successful, and in the midst of realizing their danger, the Chinese government disavows Achilles, providing evidence that he stole the missile launcher that destroyed the decoy space shuttle. Left with nowhere to turn, Achilles contacts Bean and offers the embryos in exchange for safe passage.
Bean and Peter return to the Hegemon's compound. Achilles expects Bean to be so besotted with the idea of retrieving his children that he can be killed with a bomb in the transport container for them. When Bean sees through that trap, Achilles offers up fake embryos in petri dishes, expecting to lure Bean into a vulnerable position where Bean can be killed. However, Bean has already decided that Achilles was faking and refuses to fall for any of his traps. Finally, Bean pulls out a pistol and shoots him in the eye. Thus, Achilles is killed in a similar fashion to his first victim Poke, who he killed with a knife to the eye.
The novel ends with Peter restored as Hegemon, Petra reunited with Bean, a Caliph in command of the world's Muslims, a China severely reduced in territory and forced to accept humiliating surrender terms, and the embryos still lost.
- The original name for Shadow puppets was originally conceived as Shadow of Death.