Yuki is a normal girl who reads a lot, barely talks, but really holds a lot of hidden feelings beyond her still amber eyes.
She is lonely and never had a friend. Ryouko does talk to her sometimes, but she’s too popular to bother with Yuki most of the time.
When Yuki unexpectedly befriends the exceedingly ordinary guy Kyon, who applauds Yuki for being the only girl in the school who isn’t wild and annoying, shy Yuki starts to realize she has feelings for him.
Yuki lets him into the literature club where they have small-talk conversations. Kyon feels curious about Yuki. He finds her strangely attractive, but also notices how gloomy and sad she looks. He wonders if there is something preventing Yuki from smiling. He just wants to see Yuki with a real smile.
Yuki starts writing secret stories on her computer about her and Kyon joining a club, where she’s an alien and they go on many weird adventures. The stories also include acquaintance classmates Mikuru and Koizumi, along with an imaginary character Haruhi.
(Basically, Yuki’s stories are the actual series of The Melancholy of Haruhi Suzumiya)
Kyon eventually sees the stories and thinks Yuki’s writing is interesting.
Kyon finally tells Yuki that she’s a fantastic, interesting girl and he wants to hang out with her outside of school because it’s sad seeing her so lonely.
Being with Yuki helps Kyon slowly discover a hidden side of him that really cares for her