The first central concept of Fine Structure is that the real universe in which we exist, "Alef", is one of a near-infinite array of ever-larger universes. This "Fine Structure" displays size, coherence, intelligent life and all kinds of wonders on every scale and in every conceivable cross-section. Being only 3+1-dimensional, we exist right at the very bottom of this scale.
The second major concept is that intelligence, thought, ideas and coherent information are all aspects of a superdimensional force, existing alongside gravity and electricity. Information is substance, and can be manipulated.
Information is a much more powerful force in the higher dimensions, which is why they are filled with intelligent life. In a three-dimensional universe, however, information is a very weak force, so intelligent life is rare. Humans are the only intelligent life anywhere in Alef. We are extremophiles, existing far below the point where most higher-dimensional individuals believe that intelligent life becomes impossible to sustain, like those freakish creatures which live at the ocean floor, or bacteria clinging to life in the Antarctic.
In the opening of Fine Structure, two high-D creatures, Xio (75+5D) and Oul (80+6D), go to war. Xio, the less powerful of the two, turns the tables on the other by intentionally trapping them both in Alef, a 3+1D world in which neither of them can do any damage; indeed, where sentient life, it is believed, cannot exist.
The two beings land fairly early in the universe; after the development of stars, but before any sentient life has arisen. Oul is apparently killed and Xio goes to his rest happy that his home is safe.
Then, everything goes catastrophically wrong.
As we all know, a 3+1D universe can support sentient life. Xio survives. For an extra-dimensional creature, a 3+1D prison is hell. So the task becomes escape - escape from the very "cell" which he originally built for himself.
This prison is structured with the purpose of preventing the use of super-dimensional technologies, so that no escape to higher dimensions is possible. A variety of such super-advanced technologies are initially available in Alef - technologies such as FTL communication, FTL travel, antigravity, force fields and so on. But each time a technology is used for the first time, it works only for a limited period before the "cell", which is semi-intelligent, registers this as an escape attempt and changes the rules of the universe, to block it permanently. The third major concept of Fine Structure, then, is that each technology can be used once only.
Combining all three concepts, the "A-layer" or "Eka Script" which is discovered in "On Digital Extremities" is a natural informational representation of the fundamental properties of the Structure. The Structure and the Eka Script are the same thing, presented from different perspectives. When technologies are progressively locked out, the A-layer changes to reflect this.