While flying in their plane across the ocean, looking for a strange energy source, Sonic and Tails' plane is struck by lightning! They plunge into the murky depths of the ocean...and awaken on a small island. A local, a raccoon named Marine, informs them that they are on Southern Island. With Marine and Tails' help, Sonic sets about to explore the nearby islands.

Sonic Rush Adventure is a side-scrolling adventure game, and the sequel to Sonic Rush. Sonic's goal through these platform levels is to zip through as quickly as possible. By pressing the B Button while in the air, Sonic can increase his Tension Gauge by performing aerial tricks. Pressing Y uses a Super Boost, which will allow him to plow through anything in his path at amazing speed, but drains the Tension Gauge.

When Sonic reaches the treasure chest at the end of each level, he will be given a material that can be used for construction of ships and other devices. At first, Sonic is stranded on Southern Island, but after the construction of the waterbike, he can travel to other islands and explore them. Similar to The Legend of Zelda: Phantom Hourglass, the player must plot a path to the next island using the stylus, and then provide limited control over the ship as it travels. However, Sonic has different ships, each of which are notably different from Link's steamboat.

Sonic Rush Adventure also features a Battle Mode, where players can either play locally with a friend, or across the world through Nintendo Wi-Fi Connection. Players can take each other on in a one-on-one race through various levels as each player aims to get to the end first.