His X-Ray Move in 9 starts a butterfly kick followed by a uppercut to the chin and then a high kick to the chin. The first two moves are a homage to his Fatality in the first game, the only non-fatal Fatality in the series.
When he wins a round in 9, he makes a gesture of respect and disappears in fire. That's the same thing he does in his 3 fatality, right before the arcade console falls on his opponent's head.
Scorpion's blazing skull is an homage to Ghost Rider. This comes in full circle in the Ghost Rider movie, when Ghost Rider, while atop a skyscraper, uses a chain to grab a helicopter and pull it toward him while yelling "COME HERE!".
In the official Mortal Kombat comic book, Scorpion grabs Sub-Zero and tells him to look into his eyes. This is an even clearer reference to Ghost Rider and his Penance Stare power.
After defeating Scorpion in Shaolin Monks, Scorpion gets dragged into the lava by skeletons. As his arm goes in, he gives the player a thumbs up. This is reference to Terminator 2 ending, in which the T-800 (Arnold Schwarzenegger) gives John a thumbs up before he gets engulfed by molten metal.
Deadly Alliance has a fake cereal advertisement showing Kano eating a bowl of Kan-Os.◊
Raiden's most iconic traits, namely his electric powers and his conical straw hat, were both designed after Lightning, one of the three servants of Lo Pan from the movie Big Trouble in Little China.
In his arcade ending in Mortal Kombat Vs DC Universe, Raiden finds himself being weakened under Earth's sun, but can regain his power so long as he keeps a mysterious green rock nearby; this is an inversion of how Superman's powers work.
Also in vs. DCU, his trademark Torpedo special is renamed as "The Superman".
Johnny Cage was inspired directly off of Jean-Claude Van Damme's character in the movie Bloodsport.
In 2, he had a "triple" decapitation fatality that worked like the regular one, only instead of one head, Cage knocks off three. This finisher move referenced a glitch discovered in the original Mortal Kombat, where Johnny Cage could knock off multiple heads in his fatality.
In Deadly Alliance, apparently, he was a contestant in Smash TV. From the same game, one of Johnny's films was entitled Exiting the Dragon of Death. He starred opposite Hong Kong action star Channie Jack.
In the first movie, after defeating Scorpion, there's a headshot photo signed "To my greatest fan" landing in the debris, a nod to his Friendship in 2.
The autographed headshot is also referenced in Cage's Babality animation in 9, where it's replaced by a doodle version.
In Shaolin Monks, in the fight between Liu Kang, Kung Lao, and Goro, Johnny intervenes and finishes off Goro. This is both a mirror of his rivalry with him, and a nod to the final scene of the Cage vs. Goro battle in the first movie.
Her costume redesign in 9 is interesting, however, given one of her Fatalities involves piano wire, it hints at Cammy's portrayal in Street Fighter II V.
In the Krypt of Deadly Alliance, one can unlock a picture of Lifeguard Sonya.◊ Her red bikini makes her heavily resemble Pamela Anderson of Baywatch fame.
His first Fatality in the game has him transform into a clown who uses a prop gun to surprise his opponent... then use said gun to blow off his head. Just like The Joker's Fatality from Mortal Kombat Vs DC Universe, except now with that pesky T rating out of the way...
His second Fatality in 9 (as Cyber Sub-Zero) has him latching onto his opponent in a fashion akin to a Saibaman and then self-destructing.
Since the early artwork for MK3 lacked names by which to differentiate characters, most people thought that Cyborg Smoke was actually Sub-Zero. In 9, Cyber Sub-Zero becomes a fully-realized character.
In 9, during Sub's chapter, he has a conversation that is very similar to his lines in the second movie.
The Courtyard music has been arranged into a hip-hop rendition for the Street stage in 3.
In 9, her chapter during story mode contains a scene very much like one found in Alien: Resurrection where she finds a lab filled with progressively more human half-breed clones of herself.
In 4, her facial features are modeled after Talisa Soto, the actress who portrayed Kitana in the theatrical adaptations.
Jax's fatality in Mortal Kombat 3 in which his arms turn into blades is likely a reference to the T-1000.
In MK vs. DC, his ending is very similar to Cyborg's origin story.
Kung Lao's weaponized hat gimmick was inspired by Bond's famous villian Oddjob.
Noob Saibot's 9 reveal trailer uses Ermac as his tag-team partner. This, plus his fighting style, seems to reference Annihilation, wherein Ermac spawned Noob to double-team Sonya.
In his Arcade Ladder ending, he makes a deal with Havik from Deception so that he can take over the Netherrealm. This could be a reference to how Havik started out as an alternate design for Noob named "Skab".
Noob's fighting stance in 9 is the same as Sub-Zero's in the first two games and Mythologies, referencing his status as the original Sub-Zero.
Smoke's 9 chapter has him spying on Shang Tsung and Kano behind a tree in the Living Forest, much like he did on the player back in MK2.
In his Mortal Kombat 3 ending (as Human Smoke), it says he vanished into the Living Forest to study the techniques of his rivals.
Cyrax and Sektor seems to be ripped right out of Predator. If you ever had doubts about this one, Cyber Sub-Zero from 9 makes it even more obvious.
Cyrax's self-destruct fatality has him typing some kind of sequence in a panel in his pulse, like the Predator himself. Later games show that Sektor and Cyber Sub-Zero have similar panels.
Cyrax uses a "Sabre of Light" in 4. In the PS2 games, Sektor also uses that and was renamed as "Pulse Blades": A blue one (green in Armageddon) for Cyrax, and two red ones for Sektor.
Cyrax and Sektor were called "Mustard and Ketchup" during development. In Deadly Alliance, Cyrax has a combo named Mustard and another named Ketchup in reference to this.
In the cartoon adaptation, Mortal Kombat Defenders Of The Realm, Cyrax and Sektor were respectively shown to be Asian and Black before automation. Later games (such as Cyrax's ending in Gold and the showing of Cyrax and Sektor's human forms in 9) reveal that the reverse actually applies within canon.
Speaking of Star Wars, Kabal was burnt alive, horrifically scarred, and forced to wear a respirator & hide behind a mask the rest of his life? Remind anyone else of Darth Vader?
One of the game over messages in Shaolin Monks is "Kabal says thank you very much." Aside from referencing the mission in which you can rescue him, Kabal's voice acting appears to be modeled after Elvis Presley.
Rain's costume is purple, there's also his name, and Armageddon reveals that he's a Prince. Explanation
Prince has a song called "Purple Rain".
Sheeva's arcade ending in 9 involves the Shokan taking control of Australia with the permission of world leaders. This is a possibly reference to Lex Luthor in Superman II.
Her namesake is Shiva, the (male) Hindu destroyer god with multiple limbs. Like Shiva, Sheeva has extra arms and is turned into a destroyer goddess in her Armageddon ending.
In Armaggedon, Stryker wears a very futuristic suit, giving him a passing ressemblance to the main character from Street Fighter 2010: The Final Fight, which was originally an unrelated game remodeled to serve as a spinoff for the series. It's worth noticing that in the original game, the character was actually named Stryker instead being passed off as Ken Masters.
Stryker's design in 9 serves as a visual update to his old look from 3, but also has some elements from his incarnation in Defenders of the Realm.
Overall, Stryker's design has him resemble Woody Harrelson to a good degree.
Ermac's Arcade Ladder ending in 9 reveals that one of the souls within his body is that of the late King Jerrod of Edenia (i.e. Sindel's husband and Kitana's father), who takes control of Ermac's body and returns to rule and protect Edenia alongside his family. This is a clever and very, very subtle nod to him being often paired up with Sindel in Ultimate Mortal Kombat 3 and Mortal Kombat Trilogy during Endurance matches.
Also in 9, Ermac is the only male "ninja" not in the first two games (excluding Cyrax, Sektor, and Cyber Sub-Zero) to receive a Klassic costume. This is a meta nod to the famous rumor that spanned the character in the first place.
The original Quan Chi is somehow similar to Spawn's demon-in-the-guise-of-an-evil-clown, Violator.
In the Deception intro, Quan Chi opens a portal to escape when he realizes that Raiden's going to try and kamikaze Onaga. He opens the same portal when he tags out during a tag match during 9.
Reiko's original design in Mortal Kombat 4 bears more than a passing resemblance to Nightwing.
Li Mei might have started as an Expy of Mileena, with her general appearance, use of Sai as weapons, and color scheme. From Deception onwards, Li Mei was revisited, and now has a notable smaller physique, uses a sword instead of Sais, and wears a suit of armor in battle.
Many of her Konquest mode messages in Deadly Alliance are references to different rock bands and songs performed by them. What's more, her alternate costume surely brings to mind KISS...
Her Blood Energy Drink◊ promo is a parody of most energy drinks in general.
In Mortal Kombat: Conquest, there was a character called Master Bo. Bo 'Rai Cho is clearly a reference to this man (with the other two syllables in his name forming a pun on borracho, the word "drunk" in Spanish).
Mokap (according to his a piece of artwork unlocked in the Krypt) did motion capture for a Johnny Cage movie lampshading his repeated string of deaths throughout the series called Mortal Kombat: The Death of Johnny Cage. Additionally, the film's poster◊ is an homage to other movies' posters, Army Of Darkness in the middle.
He is a tribute to Carlos Pesina, the guy who did some of the MOtionCAPture for Deadly Alliance.
One of Kenshi's combos is named "Blind Justice", a reference to comic book hero Daredevil, a likely inspiration for the character.
Kenshi also draws heavily from Zatoichi, the blind swordsman; one of the main differences between the two is that Kenshi wears a blindfold.
During 9's story mode, Kung Lao faces off against the tandem of Quan Chi & Shang Tsung, the titular Deadly Alliance. Quan Chi even remarks that Kung Lao doesn't stand a chance "against this DeadlyAlliance".
The narration in Sub-Zero's Arcade Ladder ending uses the name to refer to Subby & Scorpion.
The whole plot of the game (the heroes and villains from the DCU teaming up to fight against the heroes and villains from the MKU) may be a reference to the JLA-Avengers crossover.
Deathstroke's ending has him forming a clan of ninjas whose designs mirror several of the ninjas in the MK universe
One of his fatalities resemble the way he killed his son Jericho back in The Nineties.
He also uses a lot of Stryker's attacks.
Kano points out how The Flash's dash attacks and Super Speed remind him of Kabal.
Green Lantern's ending has the Armageddon pyramid, and Sinestro tries to take it over.
He also fights like Ermac.
Lex Luthor forms the Deadly Alliance with Quan Chi.
His fighting style is a near perfect copy of Sektor's.
In Wonder Woman's ending, she carries a dagger very reminiscent of Ashrah's one, Quan Chi's pendant, and a shield which resembles the logo of Deadly Alliance.
Darkseid's ending is very similar to the beginning of Mortal Kombat 2, where an old Shang Tsung begs for mercy to a big and manly "lord of darkness".
Catwoman's ending has her earning the power to turn into a cheetah. While this is kind of farfetched, Catwoman could've learned how to perform an "animality".
Bonus Challenge N° 34: Isn't This Marvellous (A match where you tap the screen repeatedly to fight.)
Freddy Krueger has several Fatalities that are reminiscent of the most infamous kills of his home franchise:
In one, after stabbing his opponent with both sets of claws, he drags him down into a hole that has just appeared. This is then followed by a geyser of blood, similar to how he killed Glen, Nancy's boyfriend, in the very first movie.
Another has Freddy throwing his opponent into a boiler to be burned alive. This references both his own origin (Freddy was burned alive by vigilante parents who wanted to make him pay for murdering their children) and how he killed the former Final Girl from the third movie as his second kill in the fourth movie.
Many of his combos are named after lines from the movies, such as "Now You're Playing With Power" or "Never Sleep Again".
The stage Fatality for the city stage (having the opponent run over by a car) bears a striking similarity to the ending of the fourth Final Destination movie, complete with an X-ray view despite not being an X-ray attack, and leaves a twitching beheaded corpse similar to the first death in that movie.
In Kitana's Arcade ending, the three Edenia women characters are re-united to fight for justice all over the realms; as the narrator explains this, the three characters are posed in silhouette over an orange background and as the ending fades to black, the music closes with the iconic jingle from the show.