Author's Note: I owe a lot of this story to previous pieces of fan fiction written about the Total Annihilation universe. A lot of people put a lot of creativity into thinking up realistic ways to explain in-game phenomena, and how to then fit those explanations into the basic story framework provided by the game. Because of this, most of my thinking in these terms would not have happened if I hadn't had the fanfic that went before to spark my creativity. It might take a bit of searching, but there is plenty still out there regarding this 'ancient' game, and it is worth finding and reading.
I am putting a glossary of sorts at the beginning of the story, so that anyone who is confused can check in here and read up on the basic assumptions I am making. Those of you who enjoy puzzling it out yourselves can just jump in and figure it out as you go along. I try to explain things in the story as well (for the best possible example of someone who does this very well, read Anathem by Neal Stephenson), but if it is ever too unclear, refer to the glossary.
Author's Note, February 8, 2010: It's been quite a while since I put much work into this, but with a renewed interest I am attempting to move forward. As a first step, I have been going back and updating all previous chapters. This is to serve the twin purposes of updating the original writing to adapt to changes in my own style, and to re-familiarize myself with the story. As an added note, I have played significant amounts of Supreme Commander, and am currently eagerly awaiting the release of Supreme Commander 2. Since these are both Chris Taylor games and are the 'spiritual successors' to Total Annihilation, you will probably find me straying into Supreme Commander territory. I will probably cut down on the use of unit names and start trying to describe them based on their military function (e.g. mobile artillery instead of Luger, light infantry K-bot instead of Peewee, etc), but I plan on keeping the general feel of the story intact. The ARM and Core will still be the major combatants (at least for now . . .) and the basic technological assumptions related to the 'lathes, Galactic Gates, clones and Patterns, and all the rest will remain as they are. But there will be a handy story-telling reason for the infusion of new units, too.
Author's Note, March 15, 2010: I've changed my mind again for a few major reasons - SupCom 2 was a letdown, and the basic assumptions about technology are just not compatible between the Total Annihilation universe and that of Supreme Commander. I do plan on adding in new units designed by Maritius and the other ARM soldiers, as well as some of the giant 'experimental' type units. Krogoths are just too much fun not to have more of them around . . .
ARM: One of the two major combatants in the world of Total Annihilation. When the Core first began uploading their minds into electronics, the ARM resisted the move to a machine-based consciousness and all that came with it. The ensuing war has been raging for millennia.
Core: When the technology became available to upload a mind into electronic format, the Core began pursuing this extensively. The change also brought huge cultural shifts, as would be expected from an entire culture that can exist without physical bodies. Core citizens who pilot vehicles and K-bots will typical create a 'backup' copy of their Pattern before being downloaded into a machine body and going into battle. They control the vehicle directly, as if it were their physical body.
Core Central Consciousness: Those within the Core who do not have a specific task are part of the Central Consciousness. This is seen as a humiliation, because it means ones brainpower is being used essentially as a single circuit in a massively complex, larger computer. The Central Consciousness has hardware somewhere, but guarding the location of that hardware is one of the primary goals of the Core.
Nanotechnology: Nanotechnology is the major advance which makes the sort of base-building seen in Total Annihilation possible. The assumption here is that all building is performed by a construction machine pouring nanobots onto a structure. The nanobots are microscopically tiny, programmable machines. Each is given specific orders to move to a particular location and become part of a structure, vehicle, etc. Many of the nanobots are un-sophisticated; they know just enough to move to a particular spot and became part of a wall or piece of armor. Other parts of the vehicle will be formed by more complex nanobots; electrical systems, for example. This explains the different 'tech levels' of construction vehicles.
'Lathes: This term can be used either for a nanolathe or a resource lathe. The nanolathe would be the specific machine possessed by construction equipment and the Commander. This allows these vehicles to 'lathe a structure, by pouring out nanobots. Resource lathes are used to explain the fact that aircraft don't need to refuel, or that a seemingly endless stream of nanobots can come from a single construction K-bot, or that storage tanks can be built across the map from the original base and still be functional. The assumption is that resources are teleported to these 'lathes, which refill storage tanks within vehicles and 'bots.
Teleportation: In the Total Annihilation universe (as I see it), teleportation is clearly possible. It has two constraints, however. If only one side of a teleporter is powered, the trip is one way. Both sides need to be powered to make two-way travel possible, but once the initial holes are created on both sides, the power to maintain it is essentially the same, regardless of size. Secondly, the amount of energy needed to create or maintain the 'hole' through space increases dramatically as the hole gets bigger. For example, two holes, each an inch across, are much cheaper to create and maintain that one hole two inches across. Because of this, the teleportation involved in resource 'lathes is usually on the order of single molecules. For vehicles with bigger resource needs, there will be more 'lathes, each with a hole that allows single molecules to pass through. Additionally, the resource 'lathes are one-way leading into the vehicles, and the power necessary to keep them open is provided in the storage facilities, where the resources are teleported from.
Galactic Gate: Based on the constraints of teleportation I outlined above, Galactic Gates are enormously expensive to power. They also connect single points – each Gate leads to one other Gate. Therefore, for a Commander to be sent through a gate requires a massive amount of energy in the starting location. For the gate to be opened in both directions, an equal amount of energy must be applied on the other side of the gate to open the 'hole' at both ends. Once both sides are open, however, the energy needed to maintain the open Gates is much less that the energy necessary to open them in the first place. Once a presence has been formed on a planet, the Galactic Gate will typically be opened just wide enough to allow a data cable to be run back to the original world. This allows communication between the worlds - and the exchange of news, unit designs, brainwave sets, etc - until enough power can be generated to fully open the Gate.
Cloning (Core): Because they lack physical bodies, citizens of the Core clearly cannot reproduce. This is overcome in two ways; copying and merging. Copying is the most straightforward; a citizen's Pattern is copied onto a different set of hardware, and then begins to exists as a new person, essentially. The two Patterns are, at the moment they are copied, identical people for all intents. From that moment, they begin to lead separate lives. The Core will generally try not to post two different Patterns who are from the same copy to the same base, and they try to keep them separate. But at any given moment, there may be millions of copies of the same original Pattern serving in different posts throughout the galaxy. These all come from the same core personality of a person who was uploaded from a physical body to the Central Consciousness millenia ago. Merging is an attempt to take two different Patterns and copy them into the same Pattern space. This always produces a new Pattern, but rarely produces one that is not deeply flawed in some way. The number of distinct Patterns is quite large, however, so it would be conceivable for a whole planet to be occupied by Core Patterns and none of them be copies of another.
Cloning (ARM): Clearly, the Core have an advantage in terms of creating new soldiers at a moment's notice. Because it is only feasible to send the Commander through the Galactic Gate, it was necessary to find a way to send hundreds or even thousands of soldiers along with him, but not have to take their physical bodies. ARM scientists took the same theoretical constructs that were used to make Patterns feasible and used them instead to create technology for brainwave sets. This is a way to essentially take a snapshot of a human brain's state and compress it. When a new human body is created, the brainwave set can be decompressed into the flesh-and-blood brain. In most cases this allows both body and mind to be created. Therefore, there are multiple copies of ARM citizens running around the galaxy, much like the Core, but each has a physical body. 'Natural' clones are people in essentially all respects - an adult physical body will be grown in a cloning facility, the brainwave set downloaded into it, and the combination decanted. These citizens pilot vehicles and K-bots through cockpits in the suits or vehicles, like any other human. Generally they are physically jacked into the vehicle through a mind-electronic interface. 'Standard' clones are a compromise of sorts. Instead of cockpits, these vehicles have cryogenic support hardware. A clone is grown that exists mainly of a small, stunted body and a fully-functional brain. The body and brain, with brainwave set installed, are placed in the vehicle. The mind-electronic interface allows these 'standard' clones to pilot vehicles in the same way as natural clones, but they never jack out of the vehicle. When this was first tried, it was seen as a compromise and something dangerously close to Core values, so it became part of ARM culture that 'standard clones would be, whenever possible, equipped with an 'android' body. When they were offduty and their vehicle was parked somewhere, they could interface with their android and use it to move about the base as a standard human would. 'Standard' clones are typically made necessary either by a lack of living quarters, or by some flaw in the original DNA which is incompatible with full cloning technology.
Cloning Registry: The sum-total of all brainwave sets of ARM citizens. A commander carries a subset of the Cloning Registry through the Gate. Not all citizens are worthy enough soldiers to be entered in the Cloning Registry. All ARM citizens undergo basic military training throughout their childhood and teenage years. Once a citizen is of age, they are subjected to a huge battery of tests. This ranks their aptitude for various tasks, and they may or may not undergo more specific training at this point. Eventually, worthy citizens are entered in the Cloning Registry, where a clone of themselves will be created on new worlds once the commander Gates into position.
Gate Memories (ARM): An ARM brainwave set is created when a citizen has undergone an extensive basic training, usually when they are between twenty and thirty years of age. Because of this, a brainwave set would normally have absolutely no real combat experience (though plenty of simulator training). When a person is cloned on a combat world they begin to gain combat experience. If that world survives long enough to run a data cable through the gate (or even open the gate fully), it is common for a clone's brainwave set to be sent back through the gate. This is then integrated into the personality of the brainwave set stored in the Cloning Registry. Because of this, a clone will be 'born' on a new world with Gate memories of hundreds or even thousands of battles, fought by copies of themselves on worlds throughout the Galaxy. Because so may Commanders never manage to activate a particular Gate, this is only the stories of particular clones who survive long enough to have their data sent back to the central planets. Additionally, some Gate memories are not included in the personality in the Registry, either because they are unstable or would cause too much emotional damage when decanted in a newly-cloned person.
Investigator: A Commander is the ultimate authority on the battlefield, and battlefields encompass whole worlds in the war. Commanders are also cut off from their superiors - the only people higher-ranking than a world's Commander are back through the Galactic Gates. It is rarely possible to get a Commander back through a gate for a court-martial. Because of this, the ARM instituted the Investigator program. Certain people are trained extensively and authorized as Investigators. The Commander then carries this brainwave sets, along with thousands of others, onto the new world. If a Commander's actions are called into question, the Investigator - pre-trained and pre-disposed toward searching for the truth - can be decanted in the cloning facility. They will then investigate the Commander and decide whether or not the Commander is a detriment to the ARM fight on that particular world. As there can be no replacement Commander, removing the Commander is a large step. In extreme cases, the Investigator can submit a recommendation that the brainwave set of the offending Commander be examined or even wiped from the Cloning Registry, so that copies of the Commander will never again exist in ARM space. Investigations are rarely reported; by the time a Commander has jeopardized a situation to the degree that an Investigator would be called, it is rarely possible to salvage it enough to open the Gate for data or travel. Thus, most attacks are on their way to disaster long before an Investigator arrives.