Shadow Puppets (2002), by Orson Scott Card is the sequel to Shadow of the Hegemon and the third book in the Ender's Shadow series (often called the Bean Quartet). It was originally to be called Shadow of Death.
Peter, Ender's brother, is now Hegemon of Earth. Accepting a tip from inside China, where Achilles 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, take over his network, and then turn Achilles over to some country for trial (at the time of this story, Achilles has betrayed Russia, Pakistan, and India).
Achilles is known to kill anyone who has seen him vulnerable. Bean and his friend 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 (Bean's Condition) 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. One other 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 colonization platform in space that used to be the battle school, relying on the protection of Colonel Graff, the former commander of that school, 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. 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).
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