Bean was the smallest student at the Battle School, but he became Ender Wiggin's right hand. Since then he has grown to be a power on Earth. He served the Hegemon as strategist and general in the terrible wars that followed Ender's defeat of the alien empire attacking Earth. Now he and his wife Petra yearn for a safe place to build a family - something he has never known - but there is nowhere on Earth that does not harbor his enemies - old enemies from the days in Ender's Jeesh, new enemies from the wars on Earth. To find security, Bean and Petra must once again follow in Ender's footsteps. They must leave Earth behind, in the control of the Hegemon, and look to the stars.
At this point, it's known that at least two of Bean and Petra's embryos were implanted by Volescu into other women. One of these has been found, and it is revealed that another is with a woman who believes the child to be Achilles'.
Meanwhile in conquered China, a belief is spreading that the current government has lost the Mandate of Heaven. Seizing upon this and with some very discreet aid from Mazer Rackham and the International Fleet, Han Tzu takes control of China, installing himself as its new Emperor. What intent he has now remains to be seen.
Peter Wiggin and Petra Arkanian come to visit Alai, who is now the Caliph of the Muslim League. Eventually, the two help Alai realize that he is little more than a glorified prisoner, and that others have been ruling Islam in his stead. After uncovering a conspiracy against him, Alai resolves to take a more firm control of his newfound nation, and to treat the peoples he wrested away from China as actual people, and not as animals as they were being treated before.
The rest of the story deals with Peter Wiggin working to create a world government free of war through his Free People of Earth, while Caliph Alai and Virlomi, now the virtual goddess of India, have other plans for "uniting" the world under them. Against this back-drop of world political machinations by former Battle School children is the extremely personal story of Bean, who because of his genetic modifications, finds himself running out of time before he dies, struggling to find his and Petra's missing children.
The ending finds Bean and Petra with eight children, the ninth implanted in a woman who believes Achilles is a great man and thinks that their child is his. The woman decides to leave Earth to live in a colony where she can raise Bean's child. Bean takes the children who have Anton's Key (3 of 9) and flies away on the starship Herodotus provided by the Fleet to achieve relativistic speeds and therefore stay alive long enough to find a cure, leaving Petra on Earth. After a heartbreaking good-bye, Petra finds out that Peter loves her, and so marries him so that her children will have a father. They have five more children together.