In the console versions, the player takes control of Scrat throughout the game and help guide him through each level, the player must also collect acorns and nuts and get to the end of the levels. Several animals would also help Scrat throughout his adventure, he would occasionally ally himself with some of the main characters throughout the game, the player will also occasionally take control as either Manny, Sid, or Diego in several bonus stages.
In the Game Boy Advance and Nintendo DS versions, the player takes control of Sid, Manny and Diego as they help them try to escape the flood by guiding them through six puzzle levels. The player also has to help Scrat get loads of acorns in the special "Scrat Rush" levels.