The various passwords found throughout the game. Each password has a small easter egg associated with it as well.
- Bomb #0: LXA-QNS-GDQ (shifting each letter one position forward in the alphabet, it spells "MYBROTHER", referencing Free the Soul's founder.)
- Bomb #1: BQZ-RGJ-DXR (shifting the letters spells "CRASHKEYS", the group Akane and Aoi founded to fight against Free the Soul.)
- Bomb #2: EQD-DYR-NTK (shifting the letters spells "FREEZSOUL". Free the Soul is the cult to which Dio belongs, led by Brother.)
- Bomb #3: LXQ-LHC-NMR (shifting the letters spells "MYRMIDONS", the clones of Left and loyal soldiers of Brother within Free the Soul. Dio is one of them.)
- Director's Office computer login: GTF-DM-L-016 (Luna's serial number.)
- Director's Office computer password: MIL-KEV-OLI (reversed, it spells "I Love Klim".)
- Q computer login: KURASHIKI (Akane Kurashiki, one of the masterminds behind this Nonary game as well as the previous one).
- Q computer login: JUMPYDOLL (Akane's nickname for a doll given to her by Junpei Tenmyouji, her childhood friend and a player in the second and third Nonary Games).
- "I can't believe it's not murder!" is a reference to the product "I Can't Believe It's Not Butter."
- "To each according to his needle" is a play on a quote by Karl Marx about communism.
- "Some days you just can't get rid of a bomb" is a line from the movie "Batman", based on the 1966 television series starring Adam West.
- "Who Set Up Us the Bomb" is a reference to Zero Wing, a video game noted for its Engrish-laden translation (often misquoted as "set us up the bomb").
- "Behind Blue Eyes" is a song by rock band The Who.
- "Through the Looking Glass" is the name of the sequel to Alice in Wonderland by Lewis Carroll.
- "In Root Beer Veritas" is a reference to the phrase "In Vino Veritas", Latin for "In Wine, Truth".
- "An equal and opposite reaction" is a reference to Newton's Third Law.
- "Secret Agent Woman" is a reference to the song "Secret Agent Man", most famously performed by Johnny Rivers.
- "Time After Time" is a reference to the Cyndi Lauper song of the same name.
- "Best Served Cold" is part of a proverb of unknown origin. In full, it states "revenge is a dish best served cold".
- "A certain point of view" may be a reference to a famous line from Obi-wan Kenobi in Return of the Jedi.
- An "arms race" is a competition between states to have the best armed forces or weaponry, as well as an obvious pun about Sigma himself (who has artificial arms).
The whole story also draws a few themes from Alice in Wonderland; it features a character named Alice and a white rabbit, takes place in an underground facility (a "rabbit hole", if you will), and being late is heavily punished. Likely coincidental to a degree given the established symbolism behind Lagomorph (an event in Akane and Junpei's past), but it does make you wonder...