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.
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