So... She ended up being the deus ex of networking itself, right?

She decides the best course of action is to stay in the wired as a god because she loves everyone and doesn't want to further fuck up things.
She just materializes or appears in the real world since she can and wants to see her friend. She can meet Alice anytime since she still is a god.
Also her dad is not her dad, she's software, not human offspring.
I just finished it today and this is what I got, I might be super wrong. Also amazing anime.

Lain was not a human. She was made human by Eiri. She rejected his idea of making everyone no longer need bodies and erased her human self from existence to reverse everything.

>>160011155
>Alice can meet her anytime

The series put emphasis on the idea that humans are all connected regardless of Eiri and the wired, and that before organic bodies they were originally like this. The reason Lain can visit Alice at any time is because Lain exists and has existed forever no matter what happens to her human form. An interpretation that I have that people don't tend to explore is that Lain was not software, was not human, but was that universal connection that Eiri accessed and made into a human.