- After completing Green Hill Zone, Tails says that it wasn't familiar to him. Green Hill Zone is from the original Sonic the Hedgehog, before Tails was in the series.
- When rescuing Knuckles, he performs a watered-down version of his Spiral Upper move from Sonic Adventure 2. He also (if Modern Sonic saved him) mentions that it's good to have his sanctuary back, referencing Sonic 3 & Knuckles.
- When Modern Sonic saves Rouge, she calls him "Big Blue", which was her nickname for him in Sonic Chronicles.
- After completing Chemical Plant Zone, Tails remarks how the pink water makes him "really nervous for some reason". People who played Sonic the Hedgehog 2 will likely agree with him, due to an infamous section in act 2 where the water rises, forcing Sonic and Tails to constantly jump up moving platforms to avoid drowning.
- After Classic Eggman reveals himself, Tails exclaims "Dr. Robotnik!", to which Classic Eggman replies "Nobody calls me that anymore."
- In The Stinger, Classic Eggman asks Modern Eggman if they ever win, to which Modern Eggman replies that it depends how you define "win". This is possibly a reference to Sonic Riders, in which Eggman did win, but all he got was a carpet.
- Sonic mentions to Tails that their current adventure is "no stranger than rescuing genies from magic storybooks or saving aliens in an interstellar amusement park", referencing Sonic and the Secret Rings and Sonic Colours respectively.
- After you beat Shadow, you get the fourth Chaos Emerald. This references one of Shadow's infamous lines in Shadow the Hedgehog - "Where's that DAMN fourth Chaos Emerald?"
- The introduction scene for Shadow's rival battle has Sonic and Shadow re-enacting the opening to Sonic Adventure 2 Battle, only in Final Rush instead of Radical Highway.
- Similarly, the introduction scene for the boss battle against Perfect Chaos uses some shots taken from the opening to Sonic Adventure, including the camera zooming in on Perfect Chaos's eye, which opens and focuses on the camera/player.
- When Sonic's friends appear to cheer him on in the scene before the final battle, Classic Eggman asks who Shadow and Rouge are, since they weren't in the classic games.
- In The Stinger, Classic Eggman mentions that he's thinking about getting a teaching degree. This is possibly a reference to the educational game Sonic's Schoolhouse, in which Eggman appeared as a teacher.
- In City Escape, Bark the Polarbear, Fang the Sniper (aka Nack the Weasel) and Bean the Dynamite appear on "Wanted" posters, and Mighty the Armadillo and Ray the Flying Squirrel appear on posters reading "Missing since 1993" - 1993 being the year SegaSonic the Hedgehog came out, which was Mighty and Ray's debut (and Ray's only appearance as a playable character by that point; he didn't return until Sonic Mania).
- One of the streets in Speed Highway is named 123 Omega Road, referencing E-123 Omega.
- White Wisps can be seen in the beginning of Planet Wisp. One of them dances exactly like Yacker dances on the Loading Screen of Sonic Colours.
- In Chemical Plant Zone Act 1, Sonic can sometimes outrun the screen. This is the only stage in which this can happen, and it was also possible in the original Chemical Plant Zone.
Mythology Gag / Sonic Generations