Special Stages in Sonic Rush Adventure are a series of special levels. These levels are however completely different from many other Special Stages in previous Sonic games in the fact that Sonic races against a pirate robot named Johnny on their respective waterbikes but like most others, completing the Special Stage will award the player a Chaos Emerald. Note that only Sonic is playable in these Special Stages as Blaze collects Sol Emeralds from a different method.
The method to access a Special Stage is the requirement of the player to travel out into the sea (using the hovercraft or submarine is recommended as they can travel further distances than the other vessels). While traveling through the seas, if the vessel stops somewhere along the route (shown by passing through a Goal gate without the Goal text) and the map reveals that the vessel has stopped at Johnny's face, Tails will ask the player if he/she wishes to accept Johnny's challenge. It should be noted that during the storyline at an early point, Sonic automatically encounters Johnny for a race for the first Chaos Emerald when sailing from Machine Labyrinth to Hidden Island 1.
The objective for the player is to beat Johnny to the goal in this race on the waterbike (Wave Cyclone). In many cases, Johnny will boost through the stage, leaving yellow marks behind and when the player rides through them, he/she will get a temporary boost. Johnny will then try to attack Sonic by dropping red mines and shooting green missiles at him. If the Wave Cyclone's health gauge depletes (from obstacles or Johnny's attacks) or if Johnny reaches the goal first, the race ends in failure but the player is welcome to retry the race as many times as needed. To keep in the lead, the player must continually use the Boost by collecting Rings and performing Tricks. If Johnny is behind Sonic, he may use the Boost, (shown by his icon on the top screen and the green exclamation mark on the Touch screen) in attempt to overtake Sonic. If Johnny boosts directly into Sonic, he will end up taking a lot of damage.
Especially for the later (and harder) Special Stages, it is recommended that the player upgrades the Wave Cyclone with Materials to give the player a better chance of winning.