Now, theory time:
The Accela incident at Cyberia was an urban legend. So were the Knights of the Eastern Calculus, KIDS and God.
So was Lain.
Lain being tied up in all these events was an urban legend. Lain being a master hacker was an urban legend. Lain being an AI was an urban legend. Alice and her relationship with her teacher was a nasty rumor, blamed on Lain.
'Yomoda Chisa', the girl that killed herself, was an urban legend. Yomoda Chisa, the girl that Lain spoke to, the girl that was friends with Alice, Juri and Reika after the memory-wipe, wanted to die but could not bring herself to commit suicide. So she decided to become someone else. She decided to become the protagonist of those urban legends: Lain.
The show is not told from the Chisa's perspective, nor from that of some objective observer. It is told from the perspective of Lain, the urban legend, the figment of humanity's collective imagination.
Every urban legend centred on Lain is portrayed to us as real, because from the perspective of Lain it *is* real. By 'becoming Lain', Yomoda Chisa gave her an active presence within reality: Whatever Chisa did, Lain did, because Chisa was imagining everything she did as if she was Lain. This is why we see the 'good' Lain and 'bad' Lain, because the Lain that Chisa believed in was good, whilst the Lain that some others believed in was bad.
When 'Lain erased herself from reality', that was Chisa imagining that Lain erased herself. That's why she's alive in the Lain-forgotten world, because she was never dead.
But we don't see Lain disappear, because from Lain's perspective, she didn't. From her perspective, she merely erased herself from humanity's collective memory, and continues to exist in a place outside of human perception. But she still 'exists' as those urban legends that float around the Wired, as that girl you think you've met but don't remember, as that girl in the static of the TV, as that God that loves everyone.
"Present Day, Present Time".
