Here are the references towards Mortal Kombat Mythologies: Sub-Zero and Mortal Kombat 9. For entries regarding the other games, check the Mythology Gag page. For entries related to guest fighters check the MK franchise's Shout Out page.
- Johnny Cage and Scorpion get their 9 appearances as unlockable skins, listed as their "Tournament" costumes.
- Jax, Kitana, Kung Lao, Liu Kang and Sub-Zero get "Revenant" versions, alluding to the end of 9.
- Scorpion's "Hanzo Hasashi" skin has shades of Human Cyrax.
- Daegon's cameos in the Takahashis' arcade endings gives him an appearance that is quite similar to that of Kratos (who was a Guest Fighter in the prior game) including his skin having a similar design to the Spartan though with tan and black in place of the latter's white and red.
- Johnny Cage's "Here's Johnny!" Fatality is basically a recreation of one of Shao Kahn's Fatalities from 9 with a Shout-Out to The Shining thrown in.
- One of Kotal Kahn's Brutalities involves his opponent being "toasted" under a sunlight cone. This can be seen as a reference to Nightwolf's "Ascension" Fatality.
- One of Kano's Brutalities has him stabbing his opponent in the stomach and bisecting them in half. This can also be seen as a nod towards Kratos's "Sword of Olympus" Fatality.
- One of Goro's Brutalities involves him burning his opponent alive. This is a reference to Kintaro burning Kabal alive in the Story Mode of 9.
- One of the Faction Kills for the Brotherhood of Shadows faction involves the opponent being sucked into a portal and a geyser of blood. This is a reference to Freddy Krueger's Geyser fatality.
- Kung Lao vs. Quan Chi: note Kung Lao: Quan Chi...
Quan Chi: Enjoy your last breaths.
Kung Lao: I have prevailed before, demon!
- Mileena's Mirror Match: note Mileena 1: How is this possible?
Mileena 2: Shang Tsung created many of us.
Mileena 1: And I will kill all others!
- Raiden's Mirror Match: note Raiden 1: Who are you?
Raiden 2: Raiden, protector of Chaosrealm.
Raiden 1: The flow of time has indeed changed.
- Sonya Blade vs. Kano: note Sonya Blade: You won't escape this time.
Kano: Escape? And miss all the fun?
Sonya Blade: This won't be fun.
- Sub-Zero vs. Johnny Cage: note Sub-Zero: Do you not recognize me?
Johnny Cage: How'd you get uncyberized?
Sub-Zero: The one benefit of Quan Chi's process.
- Sub-Zero vs. Ermac: note Sub-Zero: Ermac...
Ermac: Your soul is corrupted!
Sub-Zero: Not corrupted. Freed!
- Sub-Zero's Mirror Match 1: note Sub-Zero 1: Brother, is that you?
Sub-Zero 2: I am not your brother.
Sub-Zero 1: Then wearing his colors is an offence.
- Sub-Zero's Mirror Match 2: note Sub-Zero 1: You...
Sub-Zero 2: You are not worthy of the name Sub-Zero!
Sub-Zero 1: Who are you to judge?
- Sonya Blade vs. Johnny Cage note Sonya Blade: What do you want, Cage?
Johnny Cage: My hands on you, Baby.
Sonya Blade: What did I say about calling me "Baby?"
- Johnny Cage vs. Kano note Johnny Cage: Didn't you throw me off a bridge?
Kano: Guilty as charged.
Johnny Cage: It's payback time...
- Kung Lao vs. Scorpion: note Kung Lao: You eliminated me from the tournament.
Scorpion: Be grateful I did not kill you...
Kung Lao: Yes. I can now kill you.
- Sonya Blade vs. Erron Black: note Sonya Blade: The gunslinger.
Erron Black: I could take you away from all this.
Sonya Blade: I must be a jerk-magnet.
- Mileena vs. Johnny Cage: note Mileena: The failed actor.
Johnny Cage: I'm gonna get my awards and shove 'em through your skull.
Mileena: Touchy, aren't we?
- Sub-Zero vs. Kano: note Sub-Zero: We meet again, Kano
Kano: Last time you froze me!
Sub-Zero: Pity you chose to thaw out.
- Liu Kang vs. Goro: note Goro: I nearly bested you.
Liu Kang: With the aid of Shang Tsung's magic.
Goro: That is a lie!
- Sub-Zero vs. Scorpion: note Sub-Zero: Again we meet.
Scorpion: Again and always.
Sub-Zero: Again you shall suffer.
- Scorpion vs. Raiden: note Scorpion: You must restore my family.
Raiden: That ship has sailed.
Scorpion: Damn you, Thunder God!
Story mode and comics
- Near the end of the comics, Kuai Liang breaks into the Lin Kuei cloning facility, in order to defeat Sektor and Cyrax. The whole ordeal is made in the style of Mythologies: Sub-Zero.
- In chapter 1, Smoke, as he is fighting Johnny Cage, calls himself Enenra (Which, in his ending in MK9, were shadow creatures that he was one of).
- After the restoration of Jax, Sub-Zero and Scorpion's souls in the flashback of Chapter 5, Raiden heals Johnny. Cue the following dialogue: note Sonya: Is he gonna make it?
Johnny: Haven't I told you? He's a God.
- Also at the start of the same chapter, Raiden informs Sonya about the theft of Shinnok's amulet and its replacement with an elaborate forgery. This is a reference to the fake one that Quan Chi had created in Mortal Kombat Mythologies: Sub-Zero so as to keep the real one with himself. Though in this timeline, Shinnok wasn't fooled and got the real amulet back from Quan Chi.
- Quan Chi's lair, in addition to having Shao Kahn's Hammer, also has the late Outworld Emperor's battle damaged armor on display in the background. This is a reference to the last scene of 9's story mode in which Quan Chi picked up Shao Kahn's helmet while speaking with Shinnok.
- From Chapter 10 of the Story Mode: note Liu Kang: More visions, Raiden? Do you still see the future?
- Goro's non-lethal victory animation features him smearing the blood of his defeated enemy on his chest. This is in reference to an alleged Arcade Ending he had in the Komplete Edition of 9, which has been proven to be a hoax and thus deleted from the Mortal Kombat wikia since August 2015.