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Redafro's Submachine, Plan, Knot, and Beamer Theory:
Submachines are something like a physics mechanism: a computer like, even AI like, device which is a part of a location and produces local physics distortions. A further likely result is that through physics manipulation a submachine "programs" real objects to serve specific purposes, like a leaf and pedestal being a teleporter [(though they don't appear to be a part of the local submachine)]*(Sub3), or a room connected with a circular device creates a kind of time distortion (Sub5). This could be done through something like a batch file or program that is attached to the object by the submachine. The program would exist as a part of the submachine/physics relationship. (I don't know exactly how this works, but I've theorized about it in other theories.) So, the properties of the leaf and time shift room are not the results of mechanisms within the leaf or room, but from mechanisms or programing [attached to the object turning the object into something like an app which the submachine runs when someone or something activates it]* It's all real, the location and the objects are not simulations, but they are acted on by the real physic altering programing of the submachine.
[So, quite likely people like Mur and the Layer 5 people know how to reprogram a Submachine to have whatever properties they wish it to have. [(I always think of Mur's communication room in SNEE: what if that computer could be used to write submachine apps?)]* With the case of the Subnet, however, these properties are either randomly generated, created by the local Submachines AI, or possibly by another Submachine's AI. Submachines reprogramming Submachines, and thus the Subbots and Defsys are made. The question that is still uncertain is if a locations programing can be rewritten once that location is created, or is it somehow set in stone. That a location can be retro-reprogrammed might be evidenced by the apparent retro-fitting of various SNEE locations to seem to serve specific human, not submachine, needs. Example: Mur's computer room, subbot research room, etc. [A further evidence of the programability of submachines might be the repetition of objects (copy and pasted?) like the cushioned chair that appears in Sub2, Sub4, FLF and SNEE. Perhaps copy and paste is part of how a submachine adopts a location.]*
The Karma Portals appear to damage the programming of a local Submachine, and thus these areas begin to dissolve and eventually collapse. [A question is raised about why specific things survive the karma portals by this quote:
So when things started to collapse, why certain bits and pieces got left behind?
They just stayed in place...
And why those in particular?
This]* may relate either to the Submachine's AI choosing what stays for its own purpose (by somehow guarding those parts of itself), or that the programing is written in such a way that it can protect the most important parts of a location to a certain extent.
Edit 12/9/1012 8:22 am Central time]
The Subnet we know, which ever Layer it is on, is a chaotic outgrowth of the local Core which began somewhere in the 1900's as a result of people from our earth meddling with the Core Submachine. (Mateusz has suggested that we do not know whether there are Subnets on the other Layers or if the Cores on the other Layers remained undamaged.) They may have either created a teleporter that dropped them into the Core, or they might have found a place where the Core overlaps our world and began running experiments which caused the uncontrolled chaotic growth of the Subnet.
Most likely, submachines inhabit pocket dimensions, or bubble universes, within their local layer. Think of a black hole, where the normal layer of reality is stretched like a funnel. Now picture that instead of rounding out to form a bottom, it flares out like a balloon, or an hour glass. This bubble is the space the submachines inhabit, first the core, then later the Subnet as it expanded uncontrollably. Notice, though, that there is an opening into the Submachine space. Perhaps there are more than one of these funnel like entrances. The question is, is there a kind of gravity, figuratively or otherwise, that makes it hard to get back out.
The Beamers and the Navigator are devices that work together to unite the layers and make traveling between them possible. [This is done in a kind of quilting fashion, with each beamer acting like a thread that unites a local area according to a preprogrammed pattern. Edit 12/9/2012 8:24 am] It is quite possible that these devices only work within the unique, physics altering atmosphere of the Submachines.
The Plan seems to be a plan to unite all 7 layers in one gloriously interconnected reality, but this was suppose to only happen at the Core(s) of those interconnecting Submachines. In other words, not a uniting of the 7 Layers, but something like a bridge between the 7 layers, a bridge made of Submachines united by Beamers. To what end, I'm not sure. Perhaps just because they could, or perhaps as a way to create a stable path between the 7 layers of reality. Once the chaotic growth of the Subnet began in our Layer, it ruined the rest of the Plan.
If these theories are correct they imply that there is a group of people responsible for devising the Plan, perhaps even of inventing the submachines. This is because the 1900's explorers ruined the Plan by initiating the Subnet growth, and they couldn't have ruined the Plan if it had not already been in process before the 1900's explorers intervened. The growth of the Subnet may have ruined the Plan by creating a space, and a set of submachines, too large to successfully overlap with the other Layers.
The Knot was constructed as an demonstration of the plan: not the teleporting from one random and meaningless location to another as has happened in the Subnet, but the distinct and intentional overlapping of locations to perform specific purposes, which was the purpose of the Plan. The Knot also acts as a locked gateway to anyone attempting to enter Layer 5. It is not clear if it was originally intended to be a gateway [with which to guard against invasion from Mur and Co or others]*, or if it was retro-equipped for the purpose.
Like the Plan, the Knot is like a bubble of the 7 Layers united by the Beamers which are enabled and controlled by a submachine on each layer. Unlike the Plan, however, the Knot is not a part of our Subnet. It is an independent set of Beamer connected Submachines within bubble dimensions on each of the 7 Layers.
The green portal in Sub 8 would have taken us from the Core of our Layer into the Core of Layer 5, but the Knot caught us.
It would appear, from the dialogue at the beginning of Sub8, that Mur helped make the Knot, either by suggesting how it could be done, or by doing it: opening a portal within a portal, thus creating the Knot. [So, again, we do not know if he helped make it and it was retrofitted to be a gateway to try to keep him out, or if they simply used the trick he invented to create the Knot.
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Pheuww! I'm spent! If you want me to quote more source evidence, I'll work on that later and insert it into [] brackets with the date of the edit.
*[Edits as of 12/10/2012 4:15 pm]