All are in some way references to their respective characters.
- Dream - His sister's diagnosis of Reverie Syndrome, leaving her trapped in a 'dream'.
- Fire - Carlos is a firefighter. Additionally, his parents died in a house fire set by an arsonist.
- Fight - Carlos is a firefighter. May also reference his fight with Akane shortly before his death and/or his staged 'fight' with Junpei.
- Hero - As a fireman, he has saved many lives. He also sacrifices himself to protect Akane.
- Save - Carlos saves lives in his job, and is trying to save his sister. May also refer to his SHIFT ability, which has saved him and others from death on several occasions.
- Shift - The SHIFT ability, which he as well as several other Espers possess.
- Hex - In 999, she wore Bracelet number six.
- June - Her codename in 999.
- Key - Akane is part of the group "Crash Keys", which opposes Free the Soul. She's also a central protagonist in all of the trilogy's major events; a key player.
- Doll - Refers to "Jumpy Doll", a doll given to Akane by Junpei (also referenced in VLR as a password).
- Five - In 999, Junpei wore bracelet number five.
- Hate - Junpei has grown embittered and cynical in his search for Akane.
- Jump - Akane's nickname for him, "Jumpy".
- Ring - He holds onto a ring throughout the game, intending to propose to Akane (and does in one timeline).
- Quark - His adopted child in the VLR timeline.
- Age - A reference to Sean's young age at the time of his death, and/or Delta's old age.
- Bro - Delta is Phi's brother, as well as the leader of Free the Soul who uses the alias "Brother".
- Eye - Delta sees the events through Q's "eyes" (the cameras located around DCOM), and Q, being an AI located within the quantum computer, does as well.
- Self - Possibly referring to Q as a robot with a personality, or "self". Delta's alias at DCOM was "Q", and Q is under Delta's control so Q is, in effect, an extension of Delta himself.
- Kill - A reference to her secret life as a serial killer.
- Heart - The object of her obsession, as well as the reason for her serial killings.
- Rip - The name she was given by the media, "the Heart Ripper".
- Virgin - One of her victims was named Virginia. Mira herself may also be a virgin, though it's never actually confirmed.
- Fool - Probably refers to his gullible and volatile personality.
- Ice - A reference to his past - the icy lake where he was forced to dump his brother's body. Eric is also an ice cream salesman.
- Lake - He disposed of his brother's body in a lake.
- Love - He is in love with Mira.
- Poor - The state his family was left in after his mother's death. Eric is a generally pitiable person, too.
- Bird - Likely refers to her caged bird music box.
- Blue - Her eye color, as well as the color of the caged bird.
- Mom - Diana is the mother of Phi and Delta.
- Moon - Diana is the Roman goddess of the moon. Also a sly reference to her robotic double in the future, Luna (the name of Earth's moon).
- Dear - As Diana and Sigma's child, she is dear to both of them.
- Red - Phi's real hair color.
- Time - A reference to Sigma and Phi's SHIFT ability allowing them to leap through time.
- Twin - Phi is Delta's twin sister. She also has another "twin" - the original Phi duplicate sent back to 1904, whom the current-day Phi was duplicated from, resulting in her creation in 2008.
- Arm - In the VLR timeline, he loses his arms in a bomb blast and is fitted with artificial replacements.
- Dad - Sigma is the father of both Phi and Delta.
- Fate - Likely refers to the future timeline he's trying to avoid by changing the past. Or that he is "fated" to be the father of Delta and indirectly bring about a cataclysmic event.
- Milk - His last name backwards, "Klim". May also be an oblong reference to his artificial arms in VLR, which bleed a white fluid that resembles milk.
- Old - Sigma's future personality is in his body in the present.
The passwords Q uses are subtle references, too.
- 38080832 - Dividing it by two gives 19040416. Convert that to a date and you get April 16th, 1904 - the date Phi and Delta's duplicates arrived at in the past.
- 61404091 - The above date, just reversed.
Zero/Delta is fond of Latin, and uses quite a few such phrases throughout. Rough translations are provided here courtesy of the Zero Escape Wiki.
- "Desine fata deum flecti sperare precando" - Fate, and the dooming gods, are deaf to tears.
- "Mors certa, hora incerta" - Death is certain, its hour is uncertain.
- "Plaudite, acta est fabula." - Applaud, the play is over.
- "Stabat mater dolorosa." - The sorrowful mother stood.
- "Audentem Forsque Venusque iuvat." - Both love and luck help the bold.
- "Vive hodie" - Live for today.
Phi's brooch bears one as well.
- "Elapsam semel occasionem non ipse potest Iuppiter reprehendere" - Not even Jupiter can find a lost opportunity.
- Let's inhibit the virus/The truth is invisible - Phi and Sigma are here to "inhibit" the Radical-6 outbreak. However, they find much more than they bargain for when they arrive in DCOM. May also refer to the bunker's layout; rather than having three separate "blocks", they are all one and the same, with this fact covered up by a holographic projection.
- When a curious hate oozes calamity/What you choose can materialize us - Refers to Mira infecting Phi with the Radical-6 virus, seemingly for no reason (though as she is revealed to be a killer who revels in the act of murder, that probably played a role). The latter likely refers to the chain of events leading to Phi and Delta's births, and their being duplicated across timelines with the Transporter.
- Let the game end where I treat two/Together with me, Delta, we are ten. - Delta is the bunker's tenth inhabitant and stays hidden (or just unacknowledged) for much of the game. The game "ends" when Delta 'treats' Akane and Junpei to the truth behind his actions, leading to the nine participants returning to the surface in another timeline with their memories intact.
- The game's title is one as well. Zero Time Dilemma/Me, I'm Zero, I'm Delta.