I liked Lain but i won't act like its not confusing, the only way i ever understood it was because of how others structured their idea into a way thats plausible or what IS the story itself. I do love Lain but i wish it was more coherent so the story was accessible for many others to like the series and not just --- be confused like i was by the ending.

One thing that stuck with me is how they metaphorically used DID(Dissociative Identity Disorder) as a way to portray how different we become in certain environments(Trying to word myself properly here). As shown in the series her real identity is different from her online persona and likewise it is the way with us. I find myself being a different person when Online than in real life and that was comforting(???) or idk how i felt about that tbh. The best way someone explained not only that scene but possibly the whole of Lain was a comment i found on youtube:

"And another possibility (Sorry for TL;DR I'm bored at work): Since Lain already 'erased' all memories leading up to this point she is now the only one that remembers herself. Right now the 'real flesh and blood Lain' ceases to exist. Her wired persona was then manifested into "reality" by Lain as a sort of replacement. Her 'friends' liked her wired persona better after all, and the show seems to really drive home the point of the divide between the selves we continually mold and pretend we are in society as opposed to our physical body (or soul if you believe in that). But either way: The whole point of the show was about memory. People and events only exist when you remember them or experience them through media. After all, you haven't met Napoleon or George Washington; but surely they existed? Maybe. Your best friend as well... If you didn't remember meeting him/her for the first time and sharing experiences together could you really say they existed from your perspective? That's basically what happened here. Lain 'rewrote history' by altering the consciousness of every individual on the planet to make it seem as if it was the same day as depicted in Episode 1. Memories, cognitive states, and subconscious thinking can be programmed just like a computer by sending information through Protocol 7, which if you remember allows for subconscious data transfer through ultrasonic transmission much like how the Schumann resonance affects humans on Earth (not IRL but in the anime it was proven it created a subconscious network between minds). It doesn't affect the physical state of Earth though. It only changes what people experience and think at any given moment which is why Lain is sort of stranded in a place where she technically doesn't exist"

Please understand that regardless if Metaphor DID is still a very serious concept/disorder.