- Actor Allusion: Vincent Brooks from the puzzle game Catherine says a similar line to one of Sigma's quotes (albeit in the future tense). Both characters are voiced by Troy Baker.
Sigma: Gurrrraaaaaaaaaagh! I just solved the shit out of this puzzle!
Vincent: Fucking blocks... I'm gonna climb the shit outta you!
- Defictionalization: Like with the previous game, a watch shaped like the game's bracelet was made available as a pre-order bonus (lethal injection needles and futuristic drugs not included). They're a lot smaller and made of plastic, as opposed to the ones in the game which seem to be fairly large and look to be made of metal, with screens colored in a single color, rather than changing color display on a black screen, but still.
- Divorced Installment: The trust mechanic, which would dictate who would live and die, was originally going to be used for Dangan Ronpa.
- Executive Meddling:
- The reason why there's less horror elements in the game compared to the previous one was because the marketing department noticed people thought the prequel was too scary. According to Word of God, Dio was also planning on doing something worse to Clover when he caught her on the Luna path.
- Initially, Uchikoshi wanted an older protagonist for the sequel. However, the higher-ups wouldn't allow it because Japanese gamers believed that old men couldn't be awesome. He got around this by making Sigma discover that he was in his 67-year old body as a major late-game plot twist. He also had Junpei from Nine Hours, Nine Persons, Nine Doors show up as an old man, and no less badass.
- Flip-Flop of God: Word of God previously stated that he specifically asked Kinu Nishimura, the character designer, to make Phi look like a female Santa. Later, in a Q&A, he instead claimed that it was the character's designer preference to make her look similar to Santa...
- Name's the Same:
- While this Dio cannot stop time or crush people with road rollers, they're still both gigantic Jerkasses.
- The main character is also named Sigma.
- No Dub for You: In the European version. Seeing that 999 was never officially released in Europe, localizing this game was seen as too risky to pay extra for dual audionote . So in the end, it could have been worse. The Updated Re Release finally made the English dub track available worldwide.
- No Export for You: The promotional watches that were for preorders of VLR were available in America only. Good news is, they decided to make plenty more after the game's release. The bad news is, they are only available during conventions and only if Aksys shows up.
- The Other Darrin: In The Nonary Games's remaster of VLR, young Akane is voiced by Rena Strober instead of Ali Hillis, bringing this appearance in line with the character's appearances in the rest of the series.
- What Could Have Been:
- CERO bureaucracy aside, there were some concepts Uchikoshi didn't/couldn't slip in such as Dissipative system, Monty Hall problem, Gödel’s incompleteness theorems, Toxoplasmosis, Folie à deux, Capgras delusion, Fregoli delusion, Sally–Anne test, and Project MKUltra. Some of these figure in Zero Time Dilemma, though.
- The fancy clothes Zero Sr. was wearing came from an early concept art of K.