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Humanity, having begun to explore the Universe and master interplanetary spaceflight, encountered an alien race known as the "buggers" (known in later books as the "Formics"). The establishment of a human forward base in the asteroid Eros led to two wars between the species. Despite political conflict on Earth between three ruling parties (the Hegemon, Polemarch, and Strategos), a peace was established and an International Fleet (IF) formed against the buggers. In preparation for the buggers' return (dubbed the "third invasion"), the Fleet creates the Battle School: a rigorous training program for children with the best tactical minds.
Protagonist Andrew "Ender" Wiggin, though teased as a "Third" under a two-child-per-family policy, is one of the school's trainees. He has a close bond with his sister Valentine; but fears his brother Peter, a highly intelligent sociopath. After the IF removes Ender's monitoring device, presumably ending his chances of Battle School, he mortally wounds a fellow student, Stilson, but is left unaware of doing so. When explaining his actions to I.F. Colonel Hyrum Graff, Ender states his belief that, by showing superiority now, he has prevented future struggle. Graff, on hearing of this, offers Ender a place in the Battle School, situated in Earth's orbit, where Graff quickly isolates Ender from the other cadets, but encourages him to continue training despite frustration, through communications from Valentine.
The cadets participate in competitive war simulations in zero gravity, where Ender's innovations overwhelm his opponents. Graff promotes Ender to a new army composed of the newest and youngest cadets, which Ender leads to the highest prestige. Ender fights Bonzo Madrid, a jealous commander of another army, outside the simulation, and unknowingly kills him. Under Ender's leadership, several of his current and former squad members form 'Ender's Jeesh' that remain loyal to him.
On Earth, Peter Wiggin has used a global communication system to post political essays under the pseudonym "Locke", hoping to establish himself as a respected orator and thence as a powerful politician. Valentine, despite not trusting Peter, publishes alongside him as "Demosthenes". Their essays are soon taken seriously by the government. Though Graff is told their true identities, he recommends that it be kept a secret, because their writings are politically useful.
Ender, now ten years old, is promoted to Command School (on asteroid 433 Eros), skipping several years of training. There, he is tutored by a former war hero, Mazer Rackham. In what Ender believes to be a simulator, he directs human spacecraft against bugger fleets supposedly controlled by Mazer. Ender adapts to the game and, as the simulations become harder, receives members of his Jeesh as sub-commanders. Despite this, Ender becomes depressed by the simulations, by his isolation from others, and by his treatment by Mazer.
When told by Mazer that he is facing his final test, Ender finds his fleet far-outnumbered by the buggers and sacrifices most of his fighters to launch a Molecular Disruption Device, capable of destroying the entire planet, intending to earn himself expulsion from the school for his ruthlessness. The Device destroys the planet and the entire bugger fleet; but after the simulation ends, Mazer informs Ender that this—and earlier skirmishes in the "simulator"—were not simulation, but represented the actual I.F. contingent and the buggers' main fleet at their homeworld, and that Ender has terminated the war. Ender becomes more depressed on learning this and of the deaths of Stilson and Bonzo.
When he recovers, he learns that, at the end of the bugger war, Earth's powers fought among themselves. He stays on Eros as his friends return home and colonists venture to other worlds, using Eros as a way station. Among the first colonists is Valentine, who apologizes that Ender can never return to Earth, where he would become dangerous as used by Peter and other politicians. Instead, Ender joins the colony program to populate one of the buggers' former worlds. There, he discovers the dormant egg of a bugger queen, who reveals that the buggers had initially assumed humans were a non-sentient race, for want of collective consciousness, but realized their mistake too late, and requests that Ender take the egg to a new planet to colonize.
Ender takes the egg and, with information from the Queen, writes The Hive Queen under the alias "Speaker for the Dead". Peter, now the Hegemon of Earth and seventy-seven with a failing heart, requests Ender to write a book about him, which Ender titles Hegemon. The combined works create a new type of funeral, in which the Speaker for the Dead tells the whole and unapologetic story of the deceased, adopted by many on Earth and its colonies. In the end, Ender and Valentine board a series of starships and visit many worlds, looking for a safe place to establish the unborn Hive Queen.
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