To put not to fine a point on the Chako plot - a lot of sadness around Reiji and his life. Chako had feelings for Reiji in the beginning, but, after learning about Nagi and Reiji sleeping with their teacher, Chako fell into despair and took that picture when Esemori (her favorite author) was passed out as a "memento" and a way to hurt Nagi. She started starving herself as a way to make herself look like Nagi (someone she thought Reiji preferred - skinny and attractive), but, after the Tokyo trip, she's mentally gone. She's tired of the abyss that is Reiji and his sphere, so she no longer wants to die with Reiji. She wants to die with her favorite author.
Chako’s descent really hurt me the most. She was the most positive, and had dreams too. She was so full of life! But now, she’s an emaciated husk of herself.