Following the xenocide of the Formic species by his own hand (in Ender's Game ), Ender Wiggin writes a book under the pseudonym "Speaker for the Dead" called The Hive Queen , describing the life of the Formics as described to him by the dormant Formic queen which he secretly carries. The book is successful, and when Ender's brother, the Hegemon Peter Wiggin, recognizes Ender's handiwork, he asks him to write a similar book for him when he dies. Ender agrees, and writes The Hegemon after Peter's death. The two books together lead to the emergence of a new type of religious figure, the Speakers for the Dead, which any citizen may call on to speak for the recently deceased. Speakers are given access to all of the subject's files and writings, and when they speak, they do not judge the subject, but only speak about their life. Ender himself becomes a Speaker, though using his given name Andrew, as his nickname "Ender" has become an epithet across the Hundred Worlds synonymous with an ill-intended and all-destructive force (as delineated in and deduced from The Hive Queen and the Hegemon). Ender has spent much of his early adult life traveling between human colonies with his sister Valentine to find a home for the Formic queen to repopulate her species. Due to relativity, very little time has passed for Ender, while the rest of humanity has advanced thousands of years.
Three thousand years after the xenocide, humans have attempted to colonize the planet Lusitania, but find its ecological system unusual compared to other planets. Unique to the planet is a sentient species, the mammal-like Pequeninos ("small ones"), drawing the attention of many xenobiologists to the colony. Shortly after arrival, the colony was ravaged by a virus, Descolada , which wiped out many of the colonists before a remedy could be found, leaving a girl named Novinha without her parents. Novinha was taken in by father-and-son xenobiologists, Pipo and Libo, later becoming one herself. One day, she makes a discovery about Descolada being carried by every life form on Lusitania, including both the piggies and the trees; Pipo is inspired and races out to ask the piggies about it before revealing this inspiration. When Pipo does not return, they search and find his body vivisected, which they recognize as part of a death ritual the piggies give to their fallen. However, this ritual normally includes the planting of a sapling in the body, but there is no evidence this was done for Pipo, and they consider this hostile, and come to see the piggies as a potential threat. Novinha, who has come to have feelings for Libo, locks her files, fearing that Libo will make a similar conclusion and meet the same fate as Pipo. Novinha calls for a Speaker for Pipo.
Ender is presently living with Valentine and her husband on the planet Trondheim when the call for a Speaker arrives. Ender opts to go without Valentine as she is due to give birth soon. Besides the dormant Queen, Ender travels with Jane, an artificial sentience existing within the ansible computer network. By the time Ender arrives, 22 years have passed on Lusitania, during which Novinha had attempted to cancel her request for a Speaker. However, recent events have brought others to call for a Speaker. Four years prior, Libo was killed the same way Pipo was, and more recently, Marcos Ribeira, Novinha's husband, has died of a terminal disease. Ender, with Jane's help, quickly discovers that Novinha had refused to marry Libo despite her love for him and giving birth to his children– though acting as these are Marcos' – because if she had married him, her locked files would become available to him.
While performing the research for the Speaking, Ender becomes interested in the piggies, secretly crossing an electric barrier enacted by the Starways Congress following Pipo's death to speak to them. The Formic Queen reveals to Ender she has spoken telepathically to the Wives, the female elders of the piggies, and they have learned he is the original Speaker for the Dead; the Queen also reveals that Lusitania would be ideal for her species to begin anew. Ender's investigation is stymied by the mostly Catholic colonists; to gain cooperation, Jane issues a story that Novinha's eldest child Miro and his girlfriend Ouanda had taught the piggies human technology such as farming in direct violation of the Starways Congress; the Congress on learning this demands the colony be evacuated against their wishes, and that Miro and Ouanda are to be placed under arrest. The piggies convince Miro to hide among them by crossing the electric barrier; he does so but suffers neurological damage that partially paralyzes him. The colony rebels against the Congress, and severs their ansible connection. This disables the electrical barrier, and Ender and others go to find Miro with the help of a piggy named Human.
Ender meets with the Wives and they come to a treaty for co-habitation of the planet. While there, he learns of the piggies' concept of "third life"; normally on death, the body of a piggy becomes a "brothertree"; however, those that are vivisected will become "fathertrees" that are instrumental in their reproductive cycle, due to the Descolada virus. Libo and Pipo had determined this, and separately had sought to confirm this with the piggies. Each time, a piggy had offered themselves up to enter the "third life", but neither human would commit the act, so instead, the piggies performed the ritual on them. To demonstrate for Ender, Human offers himself up to enter "third life", and Ender agrees to it, witnessing the sapling spouting from Human's spine after the process. With clarity of the situation, Ender insists to the Wives that their treaty prevents the piggies from helping humans enter the "third life" as it would be considered murder.
Miro is safely returned to the colony though still paralyzed. Valentine and her family inform Ender they plan to help Lusitania with the revolt, and are traveling to help; Ender has Miro meet them half-way. Novinha, having gained understanding into the death of Pipo and Libo, is able to continue on and she and Ender marry. Later, Ender goes to plant the Formic Queen's egg as she has requested.
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