The themes dealt with in Eon include alienation, change, the hope for adaptability and survival. The interior of the Stone is at once familiar and alien, with its seven chambers containing forests, lakes, cities, the machinery that generates power and that at an earlier time developed the infinite corridor called "the Way." The corridor defies the laws of physics as known to the new arrivals from Earth, who must adapt to all the unfamiliar phenomena. Time is another important aspect. As characters move from the first to the seventh chambers and beyond, they travel by stages into the future until their own era is the distant past.

Another important theme relates to possibilities for social healing when there is willingness to forsake the past. Repressive ideology is responsible for bad decisions by the Soviets, who attack on Earth and attempt to invade the Stone. Yet when Pavel Mirsky, a Russian officer, sees the wisdom of casting aside Leninist ideals, he faces trouble from Communist die-hards within his own ranks. The value of casting off the past is communicated strongly in the novel's close, when Axis City's ruling Geshels prefer to send the city down the Way at one-third the speed of light rather than confront their foes, the Jarts.

The theme of human destiny pervades the novel, frequently interwoven with its technology-based elements. For example, dwellers in Axis City virtually attain eternal life, since their personality patterns can be altered, copied, and after several legally permitted reincarnations, stored indefinitely in "City Memory." However, identity is less free and more a product of scientific determination. Also, for all of Bear's characters individuality seems less important than the historical process, always subject to change. Protagonist Patricia Vasquez — the mathematician sent to unravel the laws of physics that govern the Stone — fails to find the identity she seeks in a parallel universe, an Earth that has undergone no nuclear holocaust. Thus Bear implies that although technology may yield staggering advances in the physical realm, it can only provide limited personal and social solutions.