In Super Hard Mode, the player traverses through all fourteen stages of the game as Team Sonic but their level layouts as well as the types of enemies have been tweaked to make this mode difficult to complete. The game saves after every stage in this mode and allows the player to resume the last stage reached by the player during gameplay. There are no specific missions in this mode other than reaching the Goal Ring, thus allowing the player to take their time as no Ranks are given. Notably, comical elements are added to the Stages in Super Hard Mode such as seagulls in Seaside Hill and an extra teleporter for the giant spiderweb room exit from the third core room in Mystic Mansion. If the player gets a Game Over or if the last saved level to be loaded is not listed, they will have to start the mode from the beginning.
- A similar mode exists in Shadow the Hedgehog called Expert Mode.
- The tutorial stage doesn't have the texture and animation files available for Super Hard Mode, instead will just load on black with the spinning frames. It can be accessed through the memory editor.
- Due to a glitch, when the player starts a new file in Super Hard Mode, Team Sonic's lives are always reset to three stocks. The number of Team Sonic's lives in this mode will still carry over to the other gameplay modes in Sonic Heroes as normal even when the player decides to quit their current progress in Super Hard Mode.
- Only one Hint Ring is present in Super Hard Mode which is located in Frog Forest, though it was most likely intended to be removed.
- As of the Gamecube prototype 10.8 version of the game, it does not have the stage P5.bin files present on disc and will not be playable all the way through to the end unless the disc image with PB.bin files have been replaced. After not pressing start, the title screen will redirect to the gameplay in Super Hard mode with Sonic and friends moving around and not going anywhere else on Seaside Hill.