Theory history: Submitted 2009-09-19, Doubtful 2009-05-20, Debunked 2009-12-21
The Project TheoryYou are Einstein, Murtaugh's cat. Mur studied your ability for interdimensional travel while you were in the lighthouse. When the lighthouse was buried in 2006, you simply teleported out.
Theory history: Submitted 2009-05-19, Still alive 2009-05-25, Likely 2011-02-26, Doubtful 2012-12-10, Likely 2014-11-22, Debunked 2016-01-13
Flash location: 411
Liz is EvilFirst of all, the so-called submachine has normal physics. The mysterious force of karma is what able to change physics instead. The submachine does, as stated in previous theories, have some awareness of what is happening inside it. However, it is only able to tell when its physics is changed, not just when something moves around inside it. Murtaugh came into the submachine (which is not at all isolated from our own world) after discovering the force of karma (I still need to explain that). This is what enabled him to travel within the submachine. However, while the submachine did not notice him at first, when he began to create portals (which he himself describes as "karma portals") it became aware of him. And it has set up certain defenses against him so that it is not disturbed further. However, as we, the player, do not have the ability to use this force (note that I'm contradicting my previous theory here), the submachine is not aware of us and so we are able to travel freely through to the defense systems at the edge of the submachine.
Theory history: Submitted 2010-05-19, Still alive 2010-05-26, Doubtful 2011-02-26, Still alive 2012-12-10, Doubtful 2014-11-22, Debunked 2016-01-13
I don't think anyone has really explored this possibility. Perhaps Liz was the betrayer, not the betrayed as most of us thought. She was once a friend of Mur (or maybe Mur only thought she was his friend), but betrayed him, and left the notes we see at the edge to turn us against Mur, and lead us into a trap. This doesn't explain why Mur wants to destroy the submachine though, unless...
Unless Liz is the submachine. Or in league with it, in any case.
She could be a real person, controlling it. Mur wants to get revenge on her, since she is using all the information he sent to her against him. Or she could be the submachine itself, and not even human. In which case we are really in trouble.
If you believe this theory, Mur is not evil but rather callous and blinded by rage, not willing to go to the effort to save us in order to get revenge. We may reconcile with him... and end up destroying Liz/the submachine altogether.