Theory history: Submitted 2011-08-08, Doubtful 2012-12-20, Debunked 2016-01-13
Sadistic AI Game TheoryThis also theorizes what "the plan" is.
The entire Subnet is a void, with the places you teleport to floating around in the void. This is most obvious in Sub7 with all the chunks of room and stuff floating in blackness. When the subnet was first created, the empty spaces were much less, but with Mur's karma portals and all the human activity, the solid places started to erode, becoming smaller.
Now, here is what I think "the plan" is:
Mur and possibly his gang want to destroy the core because they think that will free them back into the real world. However, if they do destroy the subnet, the remaining solid places will disappear and the void will fill in. They will actually NOT be free, just floating in a much worse version of the subnet until they die. The player somehow knows this and must chase Mur and stop him before he kills everyone.
Theory history: Submitted 2011-08-13, Doubtful 2012-12-20, Debunked 2016-01-13
The submachine is controlled by a sadistic AI who puts people into the subnet just so it can kill them. The AI puts its victims through puzzles (explaining how there is always a way "out" in the games) and gives them a false sense of hope that they can escape before killing them. Mur is merely a creation of the AI. In fact, all the notes and recordings in the games are merely there to decieve the victim into thinking that there are other people. The victim then proceeds to follow the notes until the cruel truth is revealled and they are killed by the AI.