Theory history: Submitted 2010-01-23, Still alive 2010-03-11, Debunked 2011-02-26
The Cipher TheoryThe submachine is the real world. there isn't anything outside of it. the submachine is our world. Liz, Mur,and everybody else are all in the submachine. Mur wants to invade the core so he can gain power over the subnet(King,President,ETC.) and rule all the people(kinda what Napoleon did over in Europe). he fools multiple people into helping him destroy it, and gain power. Liz and a few others are like a rebellion, trying to stop him. my guess is in sub7 Mur will invade the core and we will have to team up with Liz and the rest of the rebellion to unseat him from power.
Theory history: Submitted 2014-11-30, Debunked 2016-01-13
Flash location: 378
a group of explorers discovers old ruins (ancient section). they explore the ruins and build HQ (the root) they build the cipher plate transporter(early submachine) you as the player have a dream (submachine 1) while asleep the cipher thingy malfunctions and sends you to the light house. you discover mysterious notes around the light house and realize your had been sent forward in time and mur(a member of the exploration team) got sent to the light house 5 years before, updating the submachine(cipher plates) into the light house portal. you also notice that the subnet (all the portals, cipher plates connected) had expanded beyond the original 45 locations. you try the portal but something goes wrong and you get trapped in the space between the portals. you call this space the loop. after solving many puzzles you find one last note explaining that, with each puzzle you solve, you are moving farther into the subnet and farther away from reality. it also tells you mur had been there and designed a statue to get you out. you find yourself at the lab and discover that the portal had been changed to take coordinates, now expanded to 1044 possible areas instead of the original 45. you send a message to mur and he realizes what happened. he tells you to complete the training course and that you can work at the lab. you get the job and receive your first assignment. you are to explore the far side of the net, which has expanded to include this entire dimension, after finding 3 wisdom gems, only accesible by the cipher plate reader in the center, oldest part of the net.