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This is S.
This is also S.
This is NOT S. (it's typographics)
S stands for superimpose. In Konaka's scripts, it was his way of indicating that a line was to be displayed on screen as text rather than spoken.

For example, lines such as the following:

S: When you die? it really hurts, lol.

also, any time text appears on the Navi's screen, or any time the Navi speaks with Lain:

Lain: Hello, Navi.
S: Hello, Lain.

This second example is of particular note. The decision to emulate John Sculley's vision for Knowledge Navigator with the NAVI's operating system meant that some lines marked S were spoken aloud rather than merely displayed on screen as originally intended. The result is that a mysterious character called S appears in the cast credits of some episodes, voiced by Mikiko Kurihara.

S also appears in the script of episode 7 of Alice 6. That episode also contains a computer system similar to Knowledge Navigator, with a user interface facilitated by a voice-recognizing intelligent agent.

S is not to be confused with typographics.

Characters of the Serial Experiments Lain anime
Iwakura Family
Iwakura LainIwakura MihoIwakura MikaIwakura Yasuo
Kato JuriMizuki AliceYamamoto ReikaYomoda ChisaAlice's teacherLain's teacher
Masami EiriMasatsugu ShokoTakuyoshi MasuokaFreeterMen in Black
Cheshire CatProf. HodgesonNezumiMasatsugu Shou