By rotating the Analog Stick for a few moments in the Theme Select screen of the Options menu, a chime will eventually play, then a picture of the President's Secretary will appear, allowing it to be selected as a menu theme.

The game originally had a world ranking system that showed times and ranks from players around the world. There are also flags in the games files which were supposed to show what country the ranking was obtained in.

During the game's development, Tails wasn't initially planned to be a playable character and was only added for story purposes. Series creator Yuji Naka was asked several times if Tails was going to be playable, but gave different answers every time, ranging from "wait and see" to actually saying no. Eventually he was added because of an outcry amongst fans.

Many speculate that this is the reason Tails pilots a mech in-game. However, since he is fully controllable without it in the Chao Garden and through means of hacking (retaining his flying ability), it was most likely changed at a later time to prevent inconsistency with the play styles the game has to offer.

During the cut-scene where Sonic, Tails, and Amy discuss Eggman blasting a hole in the moon, there is a sign in the background which references NiGHTS from another SEGA series, Nights into dreams.

There is anti-piracy protection within the Dreamcast version of the game. If the console detects that the game is running from a copied disc and not an official GD-ROM, Eggman will be locked in death cycle at the start of his section in Cannon's Core. He'll immediately start falling through the floor, dying and respawning in the same position repeatedly. It's still possible to reach the end of the level, but visual glitches and a fixed improper camera angle will hinder the player's attempts to navigate the level.

At the start of the Dark Story when Dr. Eggman releases Shadow, a holographic message can be seen on the edge of the pit where Shadow was held that reads:


This message could be an early or unrealized hint at the existence of the Black Arms, the antagonists of the spin-off game Shadow the Hedgehog, or something similar that went unused in Sonic Adventure 2.

During the Crazy Gadget stage in the Hero Story, if Sonic enters the room with the colorful gravity block puzzle after 4 minutes have passed since the start of the level, Dr. Eggman will threaten Sonic through the ARK's intercom a second time. However, making it to the room before 4 minutes have passed will not trigger this dialogue.

The City Escape level music ("Escape from the City") actually has two versions that play during the level that sound nearly identical. The first one is the one that plays when the mission starts and features a 10 second instrumental opening and a radio directive for GUN units to capture Sonic just before the lyrics kick in, while the second version plays after Sonic gets an item in the stage and the background music restarts. The latter version is distinguished by the singer adding a "WOOOO! OH YEAH!!" vocalization at the 10 second startup of the song before the regular lyrics start and the song continues normally.

In the cutscene before the Metal Harbor stage in the Hero Story, Amy frees Sonic from a prison cell covered in chalk writing. She asks Sonic if he is responsible for it, but he runs off without giving an answer. Spoiler:The cutscene at the start of the Last Story reveals that the writings are those of Dr. Gerald Robotnik, and that the prison cell Sonic was held in was the same one where Robotnik was executed by firing squad after recording his video diary, featuring the same chalk writing in the background. It's unknown if G.U.N. would have also executed Sonic in the same place and manner.