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While trapped in the cell Sonic decides to take a nap while the warden says how secure Sonic is in the cell and on the island. Sonic meanwhile doesn't seem to care about escaping and decides to relax. Elsewhere Chris and Tanaka stop the motorboat and head out in a paddleboat so that they will not be spotted by the radar. However, the lookouts spot the boat and they wonder if the paddleboat poses a lot of threat, but as they go to stop Chris. Eggman appears and produces an emission that stops the computers from working, he hovers on the ground as Decoe and Becoe inform of the upgrades and Eggman says anything is worth the risk to get the emeralds. Shadow and Rouge appear even though Decoe and Becoe say not to trust Rouge. Eggman informs them of the plan that he will distract the guards, Shadow is ordered to blow up the entire island, while Rouge is to go after the chaos emeralds.

Eggman begins his assault and the robots are deployed to stop him, however he out maneuvers them and leads the robots away destroying them quickly. Also approaching the island is Tails and Amy seeing the action go on they land on the ground to find Shadow and Rouge. Amy mistakes Shadow for Sonic but then sees the mistake and backs away. Eggman hovers down telling Amy to back away as he opens up the compound. Tails switches the walker into the plane mode and chases Eggman. The X Tornado stays out of Eggman's weapons and keeps him busy. Amy meanwhile heads into the compound to get Sonic. Alarms are going off everywhere as each person goes after their own target.

Chris and Tanaka are making their way onto the island as they spot Eggman and Tails battling in the air. Eggman tells Tails that this is only a time out as he runs away leaving Tails a little confused as he lands back on the island. Eggman returns to the island to see what is going on while Chris and Tanaka continue their climb.

Rouge meanwhile has secured two of the emeralds while Shadow plans the detonator. Eggman says to set the detonator for fifteen minutes but when Rouge says she can get out in 5, the timer is set for ten minutes. Amy manages to find Sonic and connect a tube to the cell, the building starts going into lock-down mode as gold beetles and the flying dog is sent out. The warden goes a little crazy about the robot and thinks it's unstoppable. Amy goes to open the cell with the hammer, as a gold beetle appears Amy smashes it with the hammer knocking it out of commission. When Amy goes to free Sonic, he stops her saying he let them take him to learn more about Shadow.

Amy says she'll only tell Sonic where Shadow is if he'll take her out somewhere fun. Sonic jokes around saying that rescuing him is the fun thing. Amy tells him about Shadow and she sees the writing and Sonic says it was already there. Amy uses her hammer to break through doors while more alarms go off. As the alarms go off Tanaka has moved on leaving Chris, but he decides to move on as Sonic and Amy run out of the building. They meet Tanaka and Tails and Amy tries to see how Chris is doing, but Tails says they need to get moving. Sonic runs off to find Shadow.

As Rouge gets the third emerald the flying dog finds Rouge and engages her in a battle. Rouge makes short work of the robot while Sonic spots Shadow racing through the forest. Sonic engages Shadow, demanding answers as the two go into a battle. Once the flying dog is destroyed it sets off an explosion sealing the room doors. With only three minutes left the island begins to evacuate the island. Tanaka finds that Chris has disappeared and he and the others run off to find him. The army personal leave the island while Sonic and Shadow battle it out. Rouge contacts Shadow trying to get some help, but Shadow says he cannot help her saying he's busy. Rouge tries her best to escape herself.

Meanwhile Chris is running through the forest while Eggman contacts Shadow. Eggman orders Shadow to escape and Sonic overhears the detonation and runs off to save everyone. Just then Chris finds Shadow thinking it's Sonic. He then sees it's really Shadow who says he's going to get the chaos emeralds and uses chaos control to leave. Chris runs in to get Shadow as they both disappear with Tanaka just mere seconds from getting him, Sonic quickly picks him up. Shadow appears in the chamber and knocks Chris away getting the emeralds from Rouge. Rouge gets up and asks if he's going to leave Chris behind, Shadow doesn't care about Chris and goes to teleport again. As Chris gets up says Sonic has been arrested because of him begging Shadow for help to get Sonic. Shadow has flashbacks of Maria and he uses chaos control as a bright light flashes the island explodes.

Eggman watches the island explode and heads off. Sonic and the others escape in the X Tornado worried about Chris.