Lain receives cryptic messages about existence, God, and a coming prophecy. Meanwhile, Mika's world changes in ways both surreal and hyperreal.

Young children are acting strangely, arms outstretched and silently staring at the sky. A shocking vision suddenly appears in the skies; it looks like Lain! Determined to get to the bottom of this, Lain's investigations finally bring her to the creator of KIDS -- but what she discovers is not what she hoped for.

As the Knights activities make the evening news, a strange man named Nazumi wanders the city with machines strapped to his body. People on the WIRED are asking: ""Who is Lain"". Meanwhile, the two MIB agents take Lain to the Techibana offices where Lain's identity is challenged by a man; how well does she know her parents, her sister, herself? Can Lain answer him?