Matrix servers--the supercomputers which create the virtual reality prison of the Matrix--are, like all computers, composed in two parts: hardware and software. Each server handles the creation and upkeep of a single section of the overall global map that, as a whole, composes the virtual Earth of the Matrix.

1. Hardware: The hardware consists of a main processor, numerous sub-processors, main memory, and temporary memory.

A) The main processor is a chip the size of a late twentieth-century American quarter, suspended in an open space by means of the same matter-repulsion technology used by Zion ships. Each of the processor's billion pathways is a single silicon-hydrogen molecule chain, along which ionization passes in binary code: the electron of a the 'first' hydrogen atom in a given molecule is 'boosted' to the next higher power level by energy applied through laser transmission. In this way, the atom acts as an ion for the duration of the stimulation, despite the fact that the actual number of electrons does not change. Nature abhors a vaccum, even at a sub-molecular level; the 'boosted' electron wishes to fall back to its natural level, but cannot do so by the release of heat and light into the atmosphere because of the action of the matter-repulsion field. The energy is instead forced down the path of least resistance--the next hydrogen atom in the molecule, and so on down the chain. By regulating the stimulus, one can achieve binary communication.

B) Sub-processors work on the same principle as the main processor, but are physically mobile. Whereas the main processor generally handles the 'background' work--weather, the behavior of animals, etcetera--sub-processors are tasked with the human population itself. Each is capable of tracking and processing the actions of up to fifty thousand humans; as the population count at a given main processor rises above each multiple of fifty thousand, a new sub-processor is moved in to handle the excess. The fifty-thousand mark can be exceeded in emergencies, but this causes slowdown.

C) Main memory firstly houses the basic geography of the Matrix: buildings, mountains, lakes, and so on. Second, it houses the template coding for Agents and their equipment. These programs and data are loaded into temporary memory as needed, and the communication is one-way unless authorized by a process that includes cross-referencing sources from a random selection of temporary memory modules. This is a lengthy process, taking upwards of five seconds of real time.

D)Temporary memory is where the Matrix 'takes place', where users interact with geography loaded from main memory. Temporary memory usually works in tandem with sub-processor units; where one is found, the other is not often far away. This is not a hard-and-fast rule, however; for example, residential areas during hours of darkness are often composed of more temporary memory modules than processors, since many users are present but few are engaged in meaningful activity.

2. Software: The two subclassifications of Matrix software are Virtual Reality Engine and Agent.

A) It is worth noting that while the Virtual Reality Engine program which creates and maintains the Matrix environment contains protocols such as gravity and other laws of science, the focus is on user perception. The engine is designed specifically to put its occupants at ease; if enough users view an anomaly, the virtual reality program will adjust the current scenario to match those perceptions. In effect, each user is helping to direct the engine's activities, by sending instructions based on their perceptions and expectations. It is the ability to consciously control these instructions that allows the resistance to affect the Matrix the way they do. The process can be essentially compared to viewing an optical illusion: by making a wholly mental shift of perception, the appearance of an optical illusion can be altered in the eyes of the observer. With the knowledge that nothing that one sees is real, the Matrix can be altered in something akin to the same process.

B) The Agent is probably the machines' single most lethal creation, being dangerous to both the resistance and to the machines themselves. The threat they present to humanity is obvious; the threat to the machines is more subtle, and springs from the fact the Agents' program is geared more toward data acquisition and extrapolation than stability and loyalty. Quite simply, the amount of memory and processing power necessary to run any sort of artificial intelligence, even one as relatively simple as an Agent, is massive. It was more resource-effective to build less stable Agents that were highly effective in the short-term than more stable Agents effective in the long-term, especially since a new Agent can be turned out at any time for next to nothing. Numbers, however, cannot be a suitable replacement for genuine experience; older Agents--like the late Smith--are highly valued, and closely watched, even though older Agents run higher and higher risks of value system self-alteration. In layman's terms, the Agent program eventually begins to value its own integrity over its mission, and goes rogue; so far, there is no way for the human resistance to take advantage of this eventuality, but the day will come when the humans are able to recruit and/or reprogram Agents.