Theories by Mrkees.
Submachine Portal Resonance Theory (doubtful)Edit
Submachine Portal Resonance Theory
Portals rely on audial / possibly other resonance to function. The numbers you input are varying frequencies specifically set to activate the portal. Primitive experiments included bells, and floating cubes. A much more refined version of this bell-and-cube setup was the portal itself, as illustrated in these two images. [SNEE location 404]
Bell Deactivated http://i.imgur.com/66YbmYz.png
Bell Activated http://i.imgur.com/IWd5UP1.png
When you travel with the portal to a different location, you are actually "resonating" through the portal, just your mind goes through. This is how Mur "took" you through the arcade game from Sub1. You are not actually in the Subnet. This is why you never encounter anyone else in the Subnet, because the Subnet is an impossible idea that is visualized as a real place with real locations when your mind is present in it. When you travel through the portal, you aren't going "back" anywhere from where you came from, you are going one layer deeper into the impossible Subnet. It is unknown how Sub-Bots originally traveled through portal, but it would be likely that it is in a similar manner.
As an addendum, the sound you hear when you travel through the portal is the resonance frequency that is in the human register of sounds.