From Serial Experiments Lain wiki

Part of the plot of Serial Experiments Lain is exploring what is or is not real.

Masami Eiri believes that the Wired is an advanced upper layer of reality, and that the "real world" is only a projection of the electrical impulses in the brain or on the Wired. However, in the end, Lain chooses not to believe him. She believes that there is value in the real world in and of itself.