Shinji Ikari is a relatively normal high school student who lives with his mother Yui and father Gendo. Asuka, his childhood friend goes to his house to wake him up and go to school as usual. Shinji's school buddies Toji and Genosuke often make fun of him and Asuka because they act as boyfriend and girlfriend, something they both deny, though Asuka does feel something for him but she's never able to say it.
One day Shinji meets a gorgeous girl while protecting himself from the rain, her name is Rei Ayanami, a mysterious girl who just moved to town. When he comes back to his house, he finds Rei half naked. Completely shocked, he runs to his room. The first book ends with Shinji's mother revealing that Rei is a distant relative and that she'll be living with them for a while.