The show suddenly takes a depressing, moody turn when Nagato almost gets hit by a car.. and summer is coming up and she still hasn't made any excuses to keep seeing Kyon.
So, that near death incident caused Nagato to have an identity crisis.. she no longer feels like herself.. Instead of being a timid, bumbling idiot who's into portable games, she is now a cold, intelligent person he is really into books. Kyon tries to still treat her the same way, and she seems to be a lot less timid around him now.
When they go to the library to study together, Nagato suddenly remembers the first time they met, when Kyon helped her get a library card.. she starts realizing that her old self is slowly coming back, and is worried that it'll replace her new self. When she gets her glasses fixed, she doesn't put them on, and instead keeps her replacement glasses on because they symbolize her new self..
She starts having some really trippy symbolic dreams, where her old self's memories and her new self's memories are merging her into one person... she's worried that if this continues, her new self will... disappear