Professor Amomori calculates that LaMetal will collide with Earth on 9 September 1999, at 9:09:09 AM. This is an allusion to Leiji Matsumoto's previous work "Galaxy Express 999."
While Yayoi is canonically Professor Amamori's private secretary, in the film she serves as a teacher at Hajime's school, and lives in a high-class apartment. In Queen Millennia (1981) and the "Queen Millennia" manga, she lives on the second floor of a ramen shop, run by the couple who adopted her.
In the film, Hajime is introduced as a student of Yukino Yayoi, and eventually pilots an A6M Zero fighter plane to fight LaMetal's forces. However, in Queen Millennia (1981), he tries to act as a peacemaker between the peoples of La-Metal and Earth. Another difference is in the "Queen Millennia" manga, where he receives a cybernetic implant which increases his intelligence and enables him to fly space ships.