Things seem to be going right for Kyo - Ryoko will come back, he's finally made up with Kawaguchi, and his friends are happy. But the world itself is acting strange and Kyo finally discovers the server can only simulate a limited time period before resetting itself.

The Maihama server resets and the summer school term starts again; Ryoko returns to the server, but is hospitalized and comatose. Kyo discovers that Ryoko can only exist as herself within the Altair, which causes pain for them as well as those around them.