Warning: Wikipedia contains spoilers.
Peter Wiggin, Ender's brother, is Hegemon. Accepting a tip from inside China, where the psychotic Achilles de Flandres is held prisoner, Peter rescues 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).
Since Achilles kills anyone who has seen him vulnerable, Bean and Petra immediately escape, preparing for the coming confrontation. Bean believes Peter has underestimated Achilles, and that he is not safe unless he is hidden. During their travels, Petra convinces Bean to marry her and have children with her, finally allowing his love for her to overcome his native disgust with the genetic engineering that created him. Finding first the doctor who discovered the genetic modification that created Bean, and then the doctor who actually carried out the experiment, Bean and Petra arrange for six embryos to be created through artificial insemination; one is implanted in Petra, and the rest frozen and guarded.
At the same time, a message is passed to Bean that Han Tzu, a comrade from the battle school, did not pass the message about Achilles to Peter. Realizing the setup, Bean gets a message to Peter's parents, and they flee with Peter from the Hegemon's compound. Bean and Petra narrowly escape an assassination attempt themselves, and escape to Damascus, where another battle school comrade, Alai, is the unannounced Caliph of a nearly unified Muslim world. 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 their arrival, however, a message is sent betraying their arrival. Faking their own departure from the space station, they discover the traitor and send an unmanned shuttle instead, which is shot down over Brazil (not coincidentally, the same country where Achilles now occupies the Hegemon's compound).
In the previous novel, China conquered India and Indochina. Alai plans to liberate them by invading first China (a feint), and then India (once China has withdrawn its armies to defend the homeland).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 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 his children that he can be killed with a bomb in the transport container for them. When Bean doesn't fall for the trap, Achilles offers up fake embryos in petri dishes, expecting to lure Bean into a vulnerable position where Bean can be killed; again, Bean avoids the trap. Finally, Bean pulls out a pistol, and with Achilles begging for his life, shoots him in the head, finally destroying the greatest threat to peace that the world currently knows.
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 terrritory and forced to accept humiliating surrender terms, and five embryos still lost. Political intrigue, and an intricate story line. Also provides some insight into Theresa and John Paul Wiggin's lives (parents of Ender Wiggin)and shows that they are not the bland, boring characters shown in Ender's Game.