What the Show Actually Confirms
SPOILER!
By the end, several things are much firmer than they were at the start.
Eiri worked on Protocol 7 and preserved his consciousness in the Wired. The Knights helped shape the network events surrounding Lain. Lain can alter shared memory and reality at a scale far beyond an ordinary user. The Iwakura family arrangement was not the stable ordinary household it first appeared to be.
Why it matters
Lain is ambiguous, but not empty. Keeping track of what the show really confirms makes the remaining uncertainty more interesting instead of less.
Debut: Ep 009 - Protocol
What the Show Deliberately Does Not Reduce to One Answer
SPOILER!
The exact ontology of Lain is never compressed into a single comfortable sentence.
The show gives competing explanations, contradictory memories, different versions of Lain and characters who speak with certainty they have not earned. Even after Eiri is gone, the question 'where is the true Lain?' remains larger than a technical origin story.
Why it matters
The unresolved material is not a missing final page of exposition. It is part of the subject. A person who exists through memory, perception, bodies and networks cannot be fully explained by only one of those layers.
Debut: Ep 002 - Girls
The Second Watch Changes Which Scenes Look Like Clues
SPOILER!
On a first watch, the strange scenes feel like interruptions.
On a second watch, many of them become early versions of ideas the series later states more directly: Chisa separating body from identity, another Lain existing in other people's memories, the Navi swallowing physical space, KIDS distributing a human image across the city, and Eiri needing belief to stabilize godhood.
How you can tell
Rewatch the early Layers without asking 'what does this symbol mean?' every time. Ask instead which later problem the scene is teaching you to recognize.
Why it matters
Lain becomes clearer on rewatch without becoming less ambiguous.
Debut: Ep 001 - Weird