The world of Atlas was settled 231 years ago by a colony ship from Earth. The colonists found it to be a habitable but infertile world and still struggle to claim the land for crops. The only city on the planet is First Landing, which also serves the anchor point for the Space Elevator that connects Atlas to the orbital Platform, which was partly build out of the original colony ship. The rest of the land surface is divided into twenty holdings (well, nineteen now, ever since Franz Dokken took over the Van Petersen Holding in a bloody coup), each ruled by a hereditary landholder and connected to First Landing via maglev train lines. Justice on Atlas is centered around the Truthsayer Guild, whose members are capable of using a drug known as Veritas to read other people's minds, which they use to determine guilt or innocence of the accused. The Truthsayers are grown from unnamed embryos and are subjected to Veritas since that stage in order to accustom their bodies to the drug. One axiom of Atlas society is that the Truthsayers are infallible. Their verdict is final and cannot be appealed, and every citizen of Atlas has a right to a speedy and public Truthsayer reading.
A young Truthsayer named Kaliana is told to read the mind of Eli Strone, a former guard, accused of mass murder. Kaliana enters Strone's mind and is forced to relive the scenes of torture and murder, which he views as just punishment. Strone is incredulous, when Kaliana pronounces him guilty, and is sentenced to life imprisonment aboard OrbLab 2, and orbital facility for producing Veritas. Kaliana is distraught over the images in Strone's mind and doesn't realize how much the experience has affected her.
Troy Boren is a young man, who has recently arrived to First Landing from the Koman Holding, where his family still toils in the mines. He's working as part of the crew that handles the loading/unloading of the space elevator. His job is to properly document all the items coming off and on the elevator and submit daily reports. He ends up unintentionally forgetting to enter a whole sheet of items into his report and decides to sneak in after hours to update the report on the computer to avoid being fired and sent back to Koman. In the meantime, landholder Franz Dokken's manservant Maximilian and Cialben, another employee, sneak onto the space elevator grounds and retrieve a shipment of illegal Veritas (by Atlas law, only Truthsayers are allowed to use the drug), which Dokken plans to secretly spread among the populace of rival holdings to sow chaos. By Dokken's order, Maximilian kills Cialben and plants evidence that paints him as the smuggling ringleader. Unfortunately, Troy happens upon the body and is caught standing over it.
Troy demands a Truthsayer reading, and it's once again Kaliana's turn. Still haunted by her previous experience and unaware that her powers are fading, she misreads Troy's feelings of guilt over falsifying the report as guilt over murder and pronounces him guilty, much to the shock of Guild Master Tharion, who was assured by his mentor Dokken that the boy was innocent. Like Strone, Troy is sentenced to life imprisonment aboard OrbLab 2.
After a while, Kaliana realizes that she has made a mistake and goes to Tharion, who is conducting a private investigation into Veritas smuggling and realizes that the drug used by the Guild has been diluted on OrbLab 2. He has her stripped of her Truthsayer status, as a Truthsayer can never be wrong, and tells her that Troy can't be found publicly innocent, as that would shatter the people's faith in the Guild. Instead, he embeds her into the investigative team he sends up to OrbLab 2 and enlists the help of Kareem Sondheim, the ancient man in charge of the Platform (the so-called "landholder without land"), into helping Kaliana break Troy out (with the caveat that Troy would have to start a new life on Atlas with no connection to his past). When Franz Dokken finds out that Tharion is sending a Truthsayer to investigate the smuggling, he browbeats Sondheim into sabotaging the escape attempt to protect his protégé Dieter Pan, the man in charge of OrbLab 2, who is a key member of the smuggling ring. As Kaliana and Troy are crossing the space between OrbLab 2 and the Platform, they are attacked by Sondheim's guards using an old Plasma Cannon, left over from the SkySword, a warship sent by Earth a century or so ago to bring Atlas under military control (the attempt was thwarted thanks to Veritas). Troy and Kaliana manage to survive the attempt and make their way to the elevator. After getting to the surface, they get aboard the first train they find and jump off after a few hours. They are picked up by a crew of a prospector rover and taken to the nearest village, which happens to be in the Toth Holding, where they are enlisted into working the granite quarry.
Meanwhile, Tharion is told by Sondheim that Troy and Kaliana died in an accident during the attempt. Outside the Guild Temple, he encounters Dieter Pan and secretly reads his mind, finding out the truth. Distraught, he heads to the Dokken Holding, but doesn't find the landholder himself, who has gone to a hidden cave, where he keeps an old cryotube, which he uses to skip weeks at a time as a Human Popsicle, thus extending his lifespan. Tharion finds Maximilian in the wilderness and Mind Rapes him into revealing all of Dokken's secrets, which also leaves the manservant brain-dead. Tharion finds out that Dokken is behind Veritas smuggling, as well as countless other schemes directed at destabilizing every other holding but his own, as well as weakening the Guild. Dokken plans to be the sole ruler of Atlas by the time the next colony ship from Earth arrives in 5 years. Also, Tharion finds out that Dokken is his father.
Tharion sends secret messages to Eli Strone and set up his own escape attempt. Using his training, Strone kills Dieter Pan, overpowers two guards, and escapes to the surface. Tharion then gives Strone as a manservant to Franz Dokken as a replacement for Maximilian (Dokken things one of the other landholders killed him), hoping that the murderer would kill the scheming landholder.
The village where Troy and Kaliana are hiding out is visited by landholder Emilio Toth, who introduces his new Magistrate, a childhood friend of Kaliana's. They recognize one another, and Troy and Kaliana end up telling Toth everything that happened to them, as well as the truth Kaliana has gleamed from Dieter Pan. Toth reveals that he already knows much of what's been going on, having been secretly working with several other landholders to counter Dokken and stop him from destroying their society. At a secret Landholder Council meeting with representative of every holding but Dokken's present, Sondheim reveals all of Dokken's activities as well as his own culpability in them. The Council agrees to strip Dokken of his landholder status, by force if necessary. Deciding to force the issue, landholders Emilio Toth and Victoria Koman combine their forces and stage an invasion of the Dokken Holding, intending to capture Franz Dokken and restore Michel Van Petersen, Victoria's adopted son, to his rightful holding. Troy and Kaliana join in the assault.
After finding out about the Council's decision, Tharion heads to Dokken Holding, deciding to personally tell Franz Dokken about it. He also reveals that he was the one who killed Maximilian and read all his secrets. Dokken gives Tharion a Veritas capsule, allowing him to read his own mind. Tharion finds out that Dokken's plans run even deeper than he suspected and that he's not Dokken's son, he's his clone, one of many seeded throughout Atlas. He also finds out that the capsule also contains the deadly Mindfire strain that fries his nervous system.
The Toth/Koman force arrives to the Dokken Holding by train and is met by fierce resistance of guards loyal to Dokken (even though all guards are supposed to be loyal to the Guild alone). Emilio Toth delivers an ultimatum, explaining that his engineers have planted charges on the braking systems, which will cause the next incoming train (which is loaded with granite) to slam in the station at full speed. One of the Dokken guards shoots him in the shoulder, causing Toth to accidentally trigger the charges. The assault force manages to get away before the train arrives and blows up the station. The force then splits off. Michel Van Petersen, along with Troy and a small number of soldiers and militia, is to take Trident Falls, the planet's sole power plant in an attempt to cut off power to Dokken Holding. The rest of the force will continue to Dokken's villa. Van Petersen's team succeeds, and Troy figures out how to cut off power to just Dokken Holding, while continuing to supply the rest of Atlas. Toth and Koman meet fierce resistance in the village just outside Dokken's villa, with Dokken's guards using two of the SkySword's plasma cannons. Fortunately, cutting off the power also renders the cannons useless, and the defenders are overwhelmed.
Dokken contacts Sondheim, who tells him that he has just fired two missiles (also from the SkySword) directly at Dokken's villa but gives him fair warning, for old times' sake. As payback, Dokken triggers hidden explosives on the space elevator, gutting the Platform and sending it into an unstable orbit. Dokken orders the guards and the staff to flee, telling them he plans to stay and die in the villa. Then he and Strone leave on horseback towards his secret cave, planning on hiding out for several decades before emerging to start over. Each secretly plots to kill the other. The missiles arrive and leave a big crater where the villa used to be.
With the conflict over, Emilio Toth, Victoria Koman, Troy, and Kaliana watch the Platform's re-entry and crash, with Toth remembering witnessing the crash of the original colony ship. They mention that the people aboard OrbLab 2 are left without the means to get off or receive supplies, which means that will be dead soon. Michel Van Petersen has taken control of the Dokken Holding, unaware that he's also one of Dokken's clones.
A new combined session of the Guild and the Landholder Council is called, this time open to the public, with Troy and Kaliana occupying places of honor as thanks for their contributions. The new Guild Master Quarista (Tharion's widow) declares a restructuring to the Atlas system of justice, which is to incorporate a system ot checks and balances to ensure that no innocent is ever again judged as guilty. Troy is asked to spearhead the effort.
Some time later, a transmission from the Earth Dawn, the next ship from Earth expected to arrive in 5 years, informs the people of Atlas that the ship's crew has managed to increase the acceleration and shave 3 years off the trip. Everyone starts to prepare for the arrival and the coming changes.
