warning: Wikipedia contains spoilers
The person behind the kidnappings, Achilles--the sociopath Bean foiled in the previous novel--attempts to kill Bean and his family, but they avoid the attempt. After Bean discovers an encoded message, he works to rescue Petra and the others while helping Peter come to power under his own name so he can eventually be appointed Hegemon and work against Achilles.
When Peter publishes a column under the Locke pseudonym revealing Achilles for the physopathic muderer he is Achilles is forced to release the rest of the kidnapped Battle Schoolers but takes with him Petra. In India, Achilles plans an invasion of Burma and then Thailand. Most of Battle School graduates that came to Achilles of their own accord, arrange brute force attacks involving long supply lines. Petra arranges a different plan, expecting it never to be used because India could not afford to divert enough of an army from its border with Pakistan to make the attacks as Achilles plans. What she does not know is that Achilles plans to arrange a nonagression pact with Pakistan, leaving the troops free to leave the border. He takes her along as a hostage to the meeting, and deftly arranges just such a treaty.
Nonetheless her plan is not used, but for a different reason than Petra expects: Achilles is secretly working for China, and has arranged to have China attack India after India puts the bulk of its forces along the border of Thailand. At that point, Achilles plans to leave India for China, and continue his efforts towards world domination.
But Bean in Thailand has other plans. With the help of a special force in Thailand, Suriyawong, a fellow Battle Schooler, and Peter "Locke's" distinguished connection, he foils Achilles again, rescues Petra, and along the way, after the murder of Sister Carlotta by-of course-Achilles, learns about the secret of his genius and the doom it will bring him.