After Sonic and Blaze defeated Captain Whisker and his partner, Johnny, they ran away but Marine (who everyone thought stayed behind on Southern Island) caught up to Whisker to try and capture him but was captured herself. Tails noticed that she was captured and Whisker was about the "torture" her with the "Tickler", which is presumed to be the Ghost Titan. Tails then came up with a plan to distract Whisker, by saying that the Jeweled Scepter was "over there". While Whisker was distracted, Sonic spin dashed at the Ghost Titan's hand, freeing Marine and Blaze caught her. The player then fights the Ghost Titan.
After beating the Ghost Titan, it explodes and Sonic and Blaze narrowly escape and watch the Big Swell sink into the sea. Sonic comments that's it's finally over and the rest of the group turn to Marine and state that what she did was risky. Sonic then says that "What counts is that it all worked out fine..." and asks Blaze about the Jeweled
Scepter. Blaze believes that it might have sunk to the bottom of the sea along with the pirates. Marine then reveals that she stole the Jeweled Scepter from Whisker when he wasn't looking and everyone heads back to Southern Island and return the Jeweled Scepter to its rightful place.
However, during the credits, a mysterious figure looms over the Scepter, and a message is shown, telling the player to collect any remaining Chaos Emeralds and Sol Emeralds. By getting them all, they will unlock Deep Core where the Egg Wizard is fought.
The Ghost Titan is mainly out of reach but can be hit by one of two cannons on either side of the stage. The Ghost Titan will either use small fish-like drones (the red ones can be hit to damage the Ghost Titan directly) or the cannons on his shoulders. Either ones can be used to destroy the force field surrounding the cannons; they can also be destroyed by the player attacking it, but it was cause damage. After the force field is down, the player can enter the cannon and cross-hairs will appear. If timed right, the player will deal huge amounts of damage to the Titan. At times, the Ghost Titan will fly down and will either try to punch the player or fire gunshots; either can be used to destroy the force fields. Repeat this process until the Ghost Titan's health to down. The player must get into the cannon again and hit the head with maximum force (which with rather hard as the cross-hairs are moving faster). Once hit, the Ghost Titan will perform its final attack, two lasers that will begin at either ends of the stage. If the player touches the lasers, they'll die instantly. When the lasers get close, it's head will fall just into range for the player to jump up and hit it. The screen will go white and the player will be graded.