There are unused graphics in the game's memory that say "Seek a way out!". In the final game they were replaced with a movie featuring Junpei and the same text. It is unknown whether or not the sprites above were mere placeholders for the movie or if the sprites were scrapped in favor of the movie.

In the steam engine room, examining a barrel under the staircase four times will have Santa make a reference to Donkey Kong.

The director of the game has stated that the events of the game take place in the year 2027.

According to an interview with 999's developer, the nine main characters are based on the Enneagram of Personalites. They are:

Ace is an Achiever (3)
Snake is an Investigator (5)
Santa is an Enthusiast (7)
Clover is a Loyalist (6)
June is a Peacemaker (9)
Junpei is a Challenger (8)
Seven is a Helper (2)
Lotus is an Individualist (4)
Ninth Man is a Reformer (1)

In the kitchen, when Lotus mocks Junpei for his lack of knowledge with appetizer plates and their usage, Junpei responds with "Well excuuuuuuse me, princess", a reference to the American animated series adaptation of "The Legend of Zelda".