As Sonic, you escort Princess Elise through the desert away from Eggman's robots. This is the 2nd stage in Sonic's story and the first stage where you have to run through while carrying Princess Elise. Sonic is able to do his homing attack on all the robots regularly despite holding Elise. He's also able to run across the quick sand while carrying Elise and uses her unknown power to create a shield that keeps them from sinking. The level is a relatively short one.
As Shadow, you start off in a hover vehicle and must find your way to the ancient ruins where Mephiles the Dark is dead set on finishing him off once and for all. On the hover vehicle, you must pass through sets of pillars that rise out of the sand each time you go through the set of pillars before it. You must do this every time otherwise the door to the temple ruins will not open. Once you're in the temple you must avoid obstacles at high speeds and destroy Iblis and Mephiles spawn as they try to stop you. Once you reach a new room you then play as E-123 Omega to locate a switch to proceed. Eventually you reach the center and the goal ring where you'll have a final battle with Mephiles the Dark.
E-123 Omega isn't playable until Shadow reaches the inside of the temple. He runs through large platforming sections and fires his blasters at the robots when needed. His objective has him attempting to reach and activate switches in order for the player to continue on as Shadow the Hedgehog.
As Silver, you start off in the ancient ruins searching for Sonic. Silver uses his psychokinesis to capture stunned robots and throw them at enemies. At a later point you play as Amy Rose to locate a switch to proceed. At the end of the stage you play as Silver again and do a series of large stone ball puzzle in an attempt to get the ball in their intended holes. This is necessary for the doors of the temple to open up and take you where you need to go. Silver later returns to the desert, this time in the exterior regions, when looking for the white Emerald in the End of the World.
Amy has the ability to (somehow) turn invisible and whack the robots she comes across with her hammer. She has no jump attack so her attacks are limited to what she can do on foot.
In Sonic's story, Sonic has just defeated the Egg Cerberus and rescued Elise. However, Eggman attempts to make due on his claim to not allow Sonic and the others to get away. He sends a squadron of robots after them in order to finish Sonic off and recapture the princess. Tails buys them some time and manages to distract a good amount of the robots away from them. Sonic and Elise run through the desert and take out the amount of Eggman's robots that manage to catch up to them. They escape and head back toward the city through a grassy plain.
Dusty Desert is the final stage in Shadow's story. After Omega's confession at Wave Ocean, Team Dark headed off to Dusty Desert where they were positive Mephiles was along with his own Chaos Emerald. They manage to make it through the desert and into the temple. When they reach the center they manage to locate Mephiles and take him on for a final battle.
Silver meets up with Amy Rose the night he spots Sonic chasing after Eggman's Egg Carrier. However, she stopped him thinking he was Sonic and now she has agreed to help locate who he's looking for as a result of feeling at fault. Once they reach the desert Silver is transfixed by the beauty around the area. When he marvels at the sight Amy is confused by his fascination with a mere desert. Silver suddenly agrees to help Amy find who she's looking for and they manage to make their way through the temple in the Dusty Desert.
- Silver's ball puzzle at the end of his stage is infamous for being extraordinarily frustrating. There has been a glitch found in the game that allows Silver to jump through the top of the door at the end of the long hall where he's supposed to push a large stone ball into a hole in order to reach the goal.
- In Sonic's Very Hard version of the stage, more traps are present, but the most dramatic change is that Sonic goes through the stage by himself. Without the shield that Sonic normally uses when carrying Elise, the terrain is more dangerous since he cannot walk across the quicksand.