In Ayanami Raising Project, the player takes on the role of a NERV officer who has just been assigned to Tokyo-3. Upon meeting with Commander Gendo Ikari, he is charged with taking care of the First Child, the mysterious Evangelion pilot Rei Ayanami. It is up to the player to decide Ayanami's weekly schedule, balancing between education, duties at NERV, and leisure. The game spans approximately one year, and includes the events of the entire anime series, as well as the movie The End of Evangelion.
In the "Asuka Supplementing Project" version released for PS2 and DS, the player can also unlock a new Asuka route.