I'm not gonna lie...I've watched this episode a couple of times to just make sure I understand. This is what I think so far:
There are 3 instances of Lain:
Real world Lain
Wired Lain
and "Virus" Lain
Lain could possibly not be real(?)
The scene showing the men in black tossing Lain into her prerendered home is some proof of this
It's possible that Lain's parents saying the end is coming is also a hint at this
Mika, Lain's sister, is braindead from overflow of information from the wired.
The busy dial tone sound that Mika is making leads me to think that her mind is lost within the Wired. It could be possible that the Knights did this to her
The Chip
This was intended to create the malicious "virus" version of Lain by manipulating her memories
The Conspiracy film
The reasons for this is to set up Eiri's creation of online conciousness
Eiri was the second suicide that happened earlier in the season
It is possible that Lain is a creation of Eiri (not sure about this yet)