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In the Egyptian-themed levels, there are hieroglyphs of black dogs on the wall that are speculated to represent Morgan T. Dog (now deceased), a pet mascot of Naughty Dog. N. Sane Trilogy kept this reference intact.

On the eastern side of the map, between Boston Common and Back Bay District, there is a door to an underground bar known as the Prost Bar. Prost, translated from German, means "cheers" and the area is a reference to the TV sitcom "Cheers" which ran from the early 80's to the early 90's.

The character Jam Kuehnemund's name is a possible reference to Jan Kuehnemund, the former lead guitarist of the rock band Vixen.

A lot of Team Rose's levels end at a much earlier point than Team Sonic and Dark's. However, through the use of glitches, exploits, or cheats, it's possible to go past the goal ring with Team Rose and go to areas that are only accessible to the two other aforementioned teams. The same thing can also be done in some of Team Chaotix's levels as well.

Interestingly, the characters of both Team Rose and Chaotix have fully voiced and functioning dialogue for these normally inaccessible areas.

In the Mojave Desert stage, the second set of oil pumps on the side of the road obscure a billboard and is usually unreadable during a race. Stopping and reading the billboard will reveal the text:

"Sometimes, God takes MOMMIES
and PUPPIES away...
And sometimes...
Just sometimes...

I do"

The Hasta La Vista Station title, tagline and mission text are all references to the Terminator franchise: The title is a phrase from the original 1984 film, the tagline "I know now why you ink..." is a reference to the line "I know now why you cry" from the 1991 sequel, the use of the word "terminate" for the mission description is unique to this mission (normally it is "defeat").

In the Octo Expansion, Stations Maverick, Goose, and Iceman are named after the nicknames of the characters from the film Top Gun. The taglines for these stations "Revvin' up your Inkjet...," "Listen to its howlin' roar...," and "Jet into the danger zone..." are references to the song "Danger Zone" by Kenny Loggins, which was used in the film.

In the Octo Expansion, the many titles and taglines of stations contain references to music from the 80s-90s:
• Roll Out Station - "Rollout" by Ludacris.
• Fake Plastic Station - "Fake Plastic Trees" by Radiohead.
• Bounce with Me Station - "Can I Get A..." by Jay-Z.
• "Just go ahead now..." Spin Docto Station - "Two Princes" by Spin Doctors.
• "Just cruisin'..." Rad Ride Station - "Just Cruisin'" by Will Smith.
• "Blowin' up like it's all good." Notorious Station - "Juicy" by The Notorious B.I.G.
• "Bring da ruckus!" Phat Splatz Station - DJ Phat Beatz and "Bring da Ruckus" by the Wu-Tang Clan.
• " Step it up!" Breakdance Station - "Step It Up" by Stereo MC.
• "As 50 yellow balloons go by..." Pop Rock Station - "99 Red Balloons" by Nena.
• "Ya like to..." Move It Move It Station - "I Like to Move It" by the Outhere Brothers.
• "Stamp-collaborate and glisten!" Stamped-Up Station - "Ice Ice Baby" by Vanilla Ice.
• "Don't just stand there..." Bust 'n' Move Station - "Bust a Move" by Young MC
• "Round round round round..." Right Round Station - "You Spin Me Round (Like a Record)" by Dead or Alive.
• "Splat magic splat!" Labyrinth Station - "Magic Dance" by David Bowie.
• "Watch out now!" Ink & Watch Station - "Watch Out Now" by The Beatnuts.
• "Gettin' dizzy with it..." Don't Ralph Station - "Gettin' Jiggy wit It" by Will Smith.
• Swass 8-Ball Station - Sir Mix-a-Lot album, Swass.
• "Inkulators, mount up!" Squee-G Funk Station - "Regulate" by Warren G and his record label "G-Funk"
• "Take it easy..." Slow Ride Station - "Slow Ride" by Foghat.
• "Don't stop 'til you pop enough!" Pop Star Station - "Don't Stop 'Til You Get Enough" by Michael Jackson, who was known as "The King of Pop."
• "Who let the pods out?" Duh-Oh Station - "Who Let the Dogs Out?" by Baha Men.
• "Might as well..." Jump Station - "Jump" by Van Halen.
• "What's the dealio?" Cubular Station - "What the Dealio" by Missy Elliot.
• "Y'all bready for this?" Toastmaster Station - "Get Ready For This" by 2 Unlimited
• Ride with Me Station - "Ride wit Me" by Nelly.
• "Ink it real good!" Ink It Station - "Push It" by Salt-N-Pepa.
• "My my my my..." Can't Touch This Station - "U Can't Touch This" by MC Hammer.
• "Can't c me..." All Eyez Station - "Can't C Me" by Tupac Shakur from his album All Eyez on Me.
• "Ink-a-zig-ah..." Girl Power Station - "Wannabe" by the Spice Girls.
• "Do not miss your chance..." One-Shot Station - "Lose Yourself" by Eminem.
• "Watch your step!" Footloose Station - "Gettin' Jiggy wit It" by Will Smith.

By playing as Peachette in the final level of Peach's Castle, the real Peach will act confused before the fight plays as normal.

One of the title's mini-games is called "Dodge Fuzzy, Get Dizzy," a reference to the title of level 1-7 "Touch Fuzzy, Get Dizzy" in Super Mario World 2: Yoshi's Island.

The names of the post-game master trainers appear to be references to other outside media:
•The Pikachu master trainer Lass Iuke is a reference to voice actress Ikue Otani who voices Pikachu in the Pokemon anime.
•The Eevee master trainer Lass Aoi is a reference to Aoi Yūki, the voice actress for Eevee in the game.
•The master trainers for Zubat and Golbat, Scientist West and Scientist Keaton, are references to actors Adam West and Michael Keaton, respectively, who both played the superhero Batman.
•The master bird trainers Bird Keeper Barney, Bird Keeper Seymour, and Bird Keeper Moe, are possible references to the characters Seymour Skinner, Barney Gumble and Moe Szyslak from the animated series The Simpsons.
•The three ghost master trainers: Psychic Arin, Psychic Danny and Psychic Ross, are references to the members of the video game web series Game Grumps; Arin Hanson, Danny Avidan and Ross O'Donovan.

Ridley's orange palette swap is in reference to the villain's appearance on the box art of Super Metroid.

The license plate on Claire's motorcycle, "J2198", is a nod to Resident Evil 2's original release date, January 21st 1998.

Alice has several pocket watches underneath her maid outfit. A detail that was revealed by the character designer, Jino, and cannot be discovered playing the game.

The Conner android has several possible references to the Terminator film franchise. Conner is an "RK800" model, just as Arnold Schwarzenegger's character from the films is a "T-800" model initially. The name of the robot from the game is "Conner" which is very similar to the surname of two central characters from the films: Sarah Connor and John Connor. The Trophy for letting Conner die every way possible is called "I'll Be Back" which comes from Schwarzenegger's icon line from the first Terminator film.

In an intro dialogue with Michelangelo and Atrocitus, after Atrocitus says that he "could wear a red ring", Michelangelo will reply back saying how he "should have worn the red bandana." A reference to how Michelangelo wore a red bandana in the original Mirage Comics.

Yoshi's new Final Smash, where he summons an army of multi-colored Yoshis, is a reference to his part in the opening of Super Smash Bros. Melee.

One of Captain Cold’s Combos is called “Prison Break”, a reference to the TV show of the same name.

In an interview, Naoto Oshima was asked if the blue birds were a direct reference to the game Flicky. Oshima said yes, and also mentioned that he asked game's designer Yoji Ishii's permission to use Flickies in his work.

The sound effects Yoshi makes are noises made by Kasumi Totaka sped up.