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The episode opens with a helicopter flying in saying the suspect is secured. The suspect is Sonic and the man says that he caused trouble at Prison Island. Sonic not wanting to be captured breaks free from the helicopter and dives off the plane with a spare piece of metal, landing in a skate board dome and sliding free. Inside a base they are tracking Sonic and send some of the robots after him.
Sonic runs through the streets as the robots destroy parts of the city. Sonic dives into the sewer wondering what they think he has been done. At school Chris is asked if he's seen Sonic up close, and Chris explains a bit vaguely about Sonic as the two suddenly split up.
Back in the limo the president is informed that the new operative is settled in. He's also informed that no one was harmed from the flood in Station Square. He's informed that Sonic has escaped and Sam explains that Sonic is innocent but the aid says that the government should let go of Sonic and Sam suddenly stops the car saying he's just driving.
As a museum a dark hedgehog is spotted taking an emerald. As the robots go to try and stop him he unleashes a blast and destroys them all running off at high speed. The president is informed at the capitol saying that Sonic has been seen stealing a chaos emerald. He orders that Sonic be taken captive and orders them to go underground to get him.
Back in the apartment Chris and the others are watching TV while the news informs about the theft and shows images of the dark hedgehog. Chris thinks it's Sonic but Cream says Sonic wouldn't take anything that doesn't belong to him. Chuck thinks it's Sonic, but everyone gangs up on him. The news says that authorities have said Sonic has destroyed tanks and fled. Chris is worried, but Ella says there are explanations.
Back underground the robots flood the sewers and all other entryways. In the sewer some homeless people are talking about the theft and the ex-aid is saying it is all Sonic when he suddenly runs by with robots chasing him.
In prison island Scarlet and Stuart are heading onto the island and Stuart uses his connections to get into the island and Scarlet wonders who Stuart is really, but he doesn't say. Inside the two interview the warden and he shows some camera footage a hedgehog and Eggman attacking on the robots as they think the new hedgehog isn't the project shadow file.
In the city Sonic escapes the sewer with robots pouring after him. Suddenly one of the larger robots appears and Sonic holds up a power ring dodging the shots that are being fired at him. He goes into a spin attack and runs to escape as the robot fires missiles at him. Sonic manages to make the missile hit and destroy the robot. Just then there is a flash of light and the new hedgehog appears saying it's a pleasure to meet him. Sonic figures that it is the new hedgehog that has framed him and as he goes into attack the new one disappears. Stuart meanwhile figures that he hedgehog he's looking at isn't Sonic. Up on the roof the new hedgehog says he is not the imposter but the real thing. Sonic goes up onto the building but the new one goes to another building and Sonic challenges him to a race.
The two run neck and neck while Chuck gets a call that Sonic is battling a robot. Chris runs off and Chuck and the butler run to follow him. Sonic and the new hedgehog are busy racing while Sonic tries to pull the lead the two keep up their speed. Chris and the others catch up with Sonic as the new hedgehog hits him from behind. Eggman is busy watching the footage and says that he was overwhelmed when he encountered Shadow.
Eggman has a flashback to the event when Shadow first woke up and he pledges his loyalty to Eggman. Just then the robot appears and Shadow destroys the robot. Back in the present Eggman hopes that Shadow will destroy Sonic. Shadow holds up a chaos emerald and Sonic demands he hand over the emerald. Shadow keeps disappearing before Sonic can get to him. Shadow uses chaos control and Sonic is wondering how Shadow can do it with one emerald. The two start fighting, but Shadow one-ups Sonic and knocks him to the ground.
Shadow says he isn't using his full power and says that Gerald Robotnik gave him the power of chaos control. Just then they hear sirens and Shadow disappears as the cops arrive. Sonic is ordered to put his hands up and Sonic protests saying he didn't do it. Chris pleads with Sonic to turn himself in and Sonic when Sonic hears about Prison Island and turns himself in. Sonic thinks he'll get out without tricks and he'll meet back up with Shadow.
Sonic is taken away while Shadow says he will not let anyone stand in his way. Eggman throws a party and congratulates Shadow on doing his job. Shadow says Eggman needs more emeralds to use an Eclipse Cannon and that he'll rule the world with it. Bokkun appears with a message with Rouge on it saying they need to get together. Becoe and Decoe say no to trust her but Eggman orders them to go her. Rouge appears and shows Eggman the chaos emerald. Rouge says she'll turn it over if Eggman lets her work with them. Eggman wonders what Rouge wants while Shadow has flashbacks about Maria. Rouge asks his name and he turns saying Shadow the Hedgehog.
Back on the land Chris and Tanaka head out in disguises on the boat and Chuck says they need to be careful as Tails and Amy fly overhead in the X Tornado with Amy saying they need to get there in a hurry, Tails says she's bossy and Amy asks him what he's said Tails gets a little scared. On the island Sonic sits in a cell with water around it with odd writing on the wall as he wonders about Shadow.