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Alice is Lain's only real friend, showing her love and kindness towards the shy girl. She is like a mother to Lain, protecting her when shots rang out at Cyberia, keeping Reika and Juri in line when they get to bossy, encouraging and organizing everyone, and making sure Lain is ok. She is also much more knowledgable about the Wired, as she is aware of hacker jargon and has a pocket Navi (which she sends messages to Lain with during class...shame on you!)
Of course, Alice has her secret side. Out of everyone's view she is having a relationship with a teacher at her school (Woah!). The Knights try to use this to their advantage, using "Lain in the Wired" to tell her secret to all online and therefor ruin Lain and Alice's friendship.
However, Lain refuses to give up and fights to clear her name with Alice, erasing everyone's memory of the rumor. In the end, it is Alice who proves to Lain that, while she is software, she has emotions, has a heart, and it is their friendship that finnaly brings Lain back from the brink, keeping her from falling completely under Deus's control.