Layer 12 Analysis

Lain is actually God

There was some dialogue in Layer 12 that finally clicked inside my head that leads me to believe that Lain may in fact be the 'Creation God' reborn.

Lain: You could make the wired free from the devices. Lain: Telephones, TV, network... You could nothing without them. Eiri: Yes, they were born with human's evolution.

The NAVI and the devices like it that allowed humans to network, were a crude means of accessing an existing system. The global consciousness. This is the Wired in it's true form. The reference to John C. Lilly established this in the previous layer and it's reinforced many times throughout the anime.

Lain: A program to synchronize to the peculiar resonance of the earth in Lain: the Protocol 7. Lain: And it makes "the group of unconscious" into consciousness. Lain: Did you really invent it by yourself?

Here Lain places doubt upon Eiri's authorship of the means that allow IP7 to work. This creates a new assumption revealed in Eiri's next statements:

Eiri: What are you saying? It can't! It can't! Eiri: Do you say that there is true God!?