The asteroid itself is an elongated prolate spheroid which appears to be virtually identical to Juno, a large asteroid in the main belt. It has been hollowed out along its long axis, and subdivided into seven vast cylindrical chambers, and rotates to provide artificial gravity. The chambers are terraformed, with the second and third containing vast abandoned cities which have been maintained by automatic systems for centuries. As the Earth investigators explore the asteroid's interior, they make an even more stunning discovery — the end of the Stone's seventh chamber opens out into a vast cylindrical corridor ("The Way"), a "pocket universe" that extends far beyond the physical limit of the asteroid, and may possibly be infinite. These discoveries indicate both that the Stone's creators (who are dubbed the "Stoners") have mastered the technology to open portals into other dimensions and alternate universes, and that, for unknown reasons, these original inhabitants had been evacuated from the Stone at some time in its past, and could well be living somewhere further along the Way.
However, the momentous discovery of The Way is overshadowed by a far more pressing problem, uncovered in the records in the libraries of the abandoned cities. The investigators learn that the Stone is indeed Juno, and that it has been shaped into a massive starship by humans from Earth's future, whose ancestors had escaped a global nuclear holocaust in the early 21st century. Most disturbingly of all, they realize that these "histories" match events on present-day Earth almost precisely, and that they therefore predict Earth's immediate future — making it almost certain that a global nuclear war is imminent.
At the opening of the novel, Judith Hoffmann, head of the commission that coordinates the exploration of the Stone, recruits a brilliant young theoretical physicist, Patricia Vasquez. Hoffmann sends Vasquez to the Stone, hoping that she can unravel its secrets and perhaps find a means of altering Earth's timeline and averting the coming catastrophe. Patricia Vasquez arrives to the Stone and receives highest clearance for all the secretive information discovered by the existing science teams. She continues to absorb knowledge about all the chambers within the Stone and wonders why she is treated with such a high regard. She learns that only NATO science teams are allowed to have access to all the chambers, though on a need to know basis. Chinese and Russian science teams don't have a similar access to the whole Stone or to the discovered knowledge. Meanwhile, Russian government protests and demands a right to the recovered knowledge, while secretly training space assault teams. At the climax of the novel's first half, the Soviets secretly dispatch a secret commando force to invade and seize control of the Stone, but the NATO security troops on the Stone have been forewarned - they succeed in containing the Soviets, and Hoffman (who managed to escape from Earth just before the Death) brokers an uneasy cease-fire. However, as the two sides battle for control of the Stone, the exploration team's worst fears are realized — a full-scale nuclear war breaks out on Earth, devastating much of the planet, killing billions and triggering a nuclear winter.
Meanwhile, the descendants of the Stone's creators (who indeed live a million kilometers along the Way, and who have been secretly observing the Earthlings ever since they arrived) have realized that, thanks to advanced information gleaned from the Stone's libraries, Vasquez is now close to discovering key scientific secrets of the Stone and the Way. To forestall this, and to prevent her from falling into the hands of the Soviet forces, Vasquez is kidnapped by two of the Stone's "future" inhabitants — Olmy, a humanoid agent of the Hexamon, and his nameless colleague, an alien known as a Frant. They take her to Axis City, the main settlement of the 'Stoners' and the various alien races with whom they are cooperating. Meanwhile, four of Vasquez's colleagues are searching for her using a specially-modified V/STOL craft that is connected to a "tuberider", a device that allows the craft to be 'hitched' to the tubular singularity that runs through the center of the Way, and to travel along it at high speed. They are intercepted when they near Axis City, and reunited with Vasquez, but they soon find themselves enmeshed in the complex politics of the Hexamon, which is facing its own impending crisis, in the form of a ruthless species of alien invaders called the Jarts.
The humans who built the Stone seem to come from approximately 1,200 years in the future. Their libraries record that human civilization was nearly destroyed by "The Death", a calamitous World War involving nuclear weapons, in 2005. Events recorded in the libraries prior to The Death (with the exception of the arrival of the Stone itself) are almost identical to events occurring on Earth in the explorers' present time. Rising tensions between the U.S. and U.S.S.R., now exacerbated by both rumors of the information in the libraries and the general situation on the Stone (the Soviets and their allies have only limited access to the asteroid), suggest that not only is such a war imminent, but the appearance of the Stone may actually make it worse than recorded.
Since the Stone appears immediately prior to the recorded date of The Death, and there is no record of its own appearance at the time, the scientists reason that the Stone may come from an alternate future. Patricia Luisa Vasquez, a brilliant but naïve young theoretical physicist from Caltech, is hastily sent to the Stone to determine if The Death can be avoided on the current timeline, and to work out the mysteries of The Corridor.
A startling discovery is that the Stone is larger on the inside than outside: a corridor leading out from the seventh chamber extends beyond the end of the asteroid, and appears to go on forever. When Patricia is mysteriously abducted by a strange-looking human and an alien, an expedition is sent after her. They travel down the final chamber (called "the corridor" or "the Way"), where they encounter humanity's descendants.
The society of human descendents, called the Hexamon, live in the Axis City, a large structure on the axis of the Way, one million kilometers from the Stone, which they call Thistledown. The Hexamon is presided over by a governing body known as the Nexus. It is loosely divided into two social groups, Naderites and Geshels, based on widely differing cultural and political viewpoints.
The conservative Naderites reject much of the high technology trappings of their society for a simpler life. They are in fact, followers of Ralph Nader, whom they call "the Good Man". Nader, who was "martyred" during The Death, came to be canonized by the followers who took his name. This was largely because he opposed the technology (particularly nuclear energy) that led to the catastrophic war.
The futuristic Geshels, on the other hand, embrace all manner of technological advances including human augmentation and artificial bodies. Many radical Geshels go so far as to choose non-human (or neomorphic) shapes for themselves, as opposed to moderate ones who choose a more human (or homorphic) appearance.
The high technology of the Hexamon civilization, with their control over genetic engineering, human augmentation (including post-symbolic communication), the concept of parallel universes, alternate timelines and the manipulation of space-time itself are major themes in the latter half of the novel. The Way itself cuts across space and time: "gates" may be opened through its surface at regular intervals, which lead to space and worlds occupying other timelines, including alternate timelines for the Earth. As a result of commerce through the gates, several alien species have come to be partners of the Hexamon as well.
Information technology and "virtual" realms are another important theme. While being held as a "guest" of the Hexamon, Vasquez learns more about their culture; she discovers that (if they choose to) its citizens are fitted with implants that can store, transmit and replicate part or of all their memories and personality. This technology confers many remarkable abilities. One is that they can create virtual replicas of themselves (known as "partials" or "ghosts") that contain functional parts of their full personality and are able to operate independently, on their behalf, and then reintegrate their experiences with their original later. Even more remarkably, in the event of major injury or even death, their implants (if recoverable and undamaged) can be used to "reload" their personalities into artificially reconstructed replicas of their old bodies, or even into entirely new forms. However, many of its citizens are limited to only two "reincarnations" before their personalities are permanently "cached" in the Hexamon's vast data storage facilities, where they continue to exist perpetually in "virtual" form. The Hexamon technology is even able to reconstruct the bodies of the humans from 21st century, as the Soviet commander Mirsky discovers — when he is fatally shot in the head by his rivals during a confrontation in one of the libraries, the Stone's automatic defense and repair systems are triggered by this act of violence. The system reconstructs Mirsky's shattered skull and brain and resurrects him, but — because he lacks a Hexamon implant — it cannot recover all of his memories, and other physical and neurological functions can only be partially restored.
Conflict between political and ideological factions is another major theme. The book was published in 1985, before the fall of the Berlin Wall and the dissolution of the Soviet Union, and in Bear's projected future (the novel opens in 2005), the cold-war tensions between the Soviet bloc and the NATO countries continue into the 21st century. The arrival of the Stone further destabilizes the situation — the Soviets suspect that the US and its allies are controlling the Stone to gain exclusive access to advanced weapons and technology, and in the first half of the book this accelerates the world's inexorable descent into an all-out nuclear war. In the second half of the book, the theme of ideological conflict is continued through the growing tensions between the hardline political officers assigned to the Soviet force, and their more moderate military leader, Mirsky, who (like Vasquez) gains life-changing insights into the real situation that faces them after being exposed to the accelerated learning facilities of the Stone's libraries. These themes are further explored as we learn more about the rivalries between the two major factions of the "Stoners" — the more radical, pro-technology Geshel, and the more conservative and predominantly anti-technological Naderites, named in honor of 20th century consumer rights advocate Ralph Nader (who, in Bear's fictional future, was martyred in the wake of the nuclear war).
Another major theme (which Bear also explores in other novels) is the Hexamon's ongoing war with a highly advanced and implacably aggressive alien race known as the Jarts, who have entered and taken control of large sections of the Way, beyond the 2x10^9 kilometer (2 billion kilometer) point. Unknown to its creators, the Jarts were able to open a gate into the Way, where they settled and spread for three hundred years before the descendants of the Stone's original human occupants evacuated the Stone and moved along the Way. Their first encounter with the Jarts resulted in a major war that ended in a stalemate, and in the second half of the book it is revealed that the Jarts are on the verge of breaking through the Hexamon's defenses. In the novel's final climax, the Jarts launch an all-out offensive to destroy the Hexamon by opening a gate directly into the heart of a star, allowing superheated plasma to enter and blast along the Way, destroying everything in its path.
To counter the threat, a coalition of the Geshel faction and "liberal" Naderites seizes control of the Nexus and launches a daring but highly risky plan to save the Hexamon culture and destroy the Jarts who occupy the Way. They take over both Axis City and the Stone, and after evacuating the Stone for safety, they give the Hexamon's inhabitants and the 21st century humans a choice between two means of escape — either fleeing back up the Way in two of the self-contained Axis habitats, Axis Nader and Central City (which can travel along the Way's central singularity), or staying in the "present day" solar system, with the Stone and the other two Axis habitats, Axis Thoreau and Axis Euclid.
The first part of their plan involves hitching Axis Nader and Central City units to the tube-like singularity that runs through the center of the Way, and accelerating them to near light-speed. The Hexamon scientists theorize that the time-space shockwave generated by their massive acceleration will act as a sort of "battering ram", protecting them from the oncoming blast of stellar plasma, while simultaneously sealing all the open gates along the Way and destroying all the occupying Jarts. The other half of the plan requires the separation of the Stone and the Way — after triggering massive explosive charges to blow the cap off the end of the asteroid and sever the junction between them, they reactivate the Stone's engines to steer it clear of the Way, and eject Axis Euclid and Axis Thoreau out into 'normal' space, where they will join the Stone in permanent Earth orbit, after which the open end of the Way will seal itself, closing off access between it and the 21st-century Earth timeline — although the possibility remains that the machinery in the Stone's sixth chamber could be used to reconnect the Stone and the Way in the future.
Meanwhile, the "old Earth" humans in Axis City must also make their escape. The rescue party sent to find Vasquez returns to the end of the Way aboard their V/STOL - hitched to a new "tuberider", they must race ahead of the coming destruction to reach the rapidly closing aperture of the Way. But Vasquez hopes to find a way to return to "her" Earth timeline, before the Death. During her internment with the Hexamon, she has been taught the technique of opening new gates out of the Way, and she has been given a "clavicle", an advanced Hexamon device that allows her to locate and open these trans-dimensional portals. With the star plasma rushing towards her position, Vasquez frantically searches through the complex enfolding space-time geometry in the wall of the Way, and with only moments to spare she passes through in a protective capsule — only to find that she has chosen the wrong gate and has landed in an alternate Earth timeline.
In 2007, CGSociety organised a "CG Challenge" based upon Eon, with the tagline "Worlds Within Worlds". This produced many 2-d and 3-d illustrations, as well as several mock film trailers.