Theories by Bit.
Cyberspace Theory (debunked)
The 'Submachine' is actually an interpretation of Ethernet, or 'cyberspace'.
Going back to FLF, there were many references to losing memories. However there's no real back story available to explain why the memories were lost. I suspect that whatever caused this was possibly some horrible accident that left the subject nearing a vegetable state. With imminent loss of brain function, a group of scientists lead by Murtaugh were able to download or partially download the player's consciousness into a computer (note the author's affinity for the movie TRON). The 'Submachine' is actually how the mind would see or interpret the complex jumble of signals that would comprise a computer network. Much in the same fashion how the brain interprets the random firing of neurons during a dream state. So the Submachine is like a static dream state where odd things and places are found, but they all seem to interact and function in a purposeful and coherent fashion. If you consider computer hardware or software and how things work and inter react it looks much like a machine. State machines, interfaces, stacks, storage elements, gates, all working together in concert, like clockwork, and for some common purpose such as keeping time.
The memories found in FLF must be either remnants of what is left of the player's consciousness, or perhaps implanted and uploaded to the network by the science team and stored there for the player to retrieve. This is why they seem digitized and also why it is easy to move from a sterile lab into the memories while existing and interacting with what's there. While experimenting, Mur must have discovered that the player's consciousness was not only able to exist and interact with the computer network, but also heuristically make changes above and beyond the scope of the normal programming algorithms.
So for some nefarious purpose Mur decides to 'enlist' the player to take on a challenge which involves hacking into some foreign network and either bring it down or release routing restrictions to the point where network packets can flow freely. Eager for a purpose and to solve puzzles, the player agrees to the challenge and begins to manipulate the network such as to hack into such mainframe. Realizing too late what Mur really has in mind, the player is unable to backtrack and instead must complete the task before escaping.
Some other notes:
- In the game it was asked why the player doesn't see anyone else in the game. This could be because no two programs can occupy the exact same space in memory. Or it could be that the routers and switches shield the player from packet collisions and gracefully mitigate. There is communication from other players or entities in the network in the form of notes and drawings. These could be semaphores or locks between the programs.