Sonic the Hedgehog, Tails, Amy Rose, Tekno the Canary, Shortfuse the Cybernik and Johnny Lightfoot have gathered in the Emerald Hill Zone, for Sonic has a speech to make. With Doctor Robotnik defeated and missing, Sonic suggests that the Freedom Fighters should storm his Flickies' Island base, hoping to wipe it out. Everyone is keen, but Johnny suggests that he stays behind to guard the Zone and Sonic agrees, knowing there are plenty of other "nutters" than Robotnik. As the others charge off, however, Johnny presses a button on his belt and teleports away. Soon, over the ocean, Tekno revels in the fact that they'll be able to surprise any Badnik presence on the island. Unfortunately, it is the heroes that are surprised as a massive Badnik army intercepts them in mid-air. As the robots surround them, Shortfuse realises it was an ambush and is soon shot out of the air. Amy realises her crossbow has been sabotaged, leaving her unable to shoot. Worse still, Tekno's sky scooter's engines have cut out! The girls abandon ship but are quickly captured by an Octus. Sonic and Tails are the only heroes left but the bi-plane is on fire. The two leap into battle as Tails thinks that every Badnik on the planet is here. Sonic supposes they were set up, but is shot down by a Buzzor before he can think anymore.
A while later, Sonic wakes up, finding himself strapped to a bulky contraption. Coming into focus, the hedgehog discovers that it was Agent X behind the surprise attack but Tails (with the others, in a cage) doesn't know how he knew they were coming. X reveals it was because he teleported here after the meeting and, to everyone's shock, lowers his hood to discover Agent X to be Johnny! Amy is disbeliving but Tekno uses her scanner to prove that the villain really is their friend. Agent X regrets not having Robotnik here to see his greatest victory but no matter, as he pulls a lever that makes Sonic disappear into nothingness. Tails is disconsolate, but Tekno thinks that the machine might actually be a matter transporter, suggesting Sonic is still alive. Somewhere...
Sure enough, Sonic wakes up in a Shadow Dimension. Weirder still, he comes face to face with Johnny, suggesting that the rabbit on Mobius is actually a fake. Johnny tells his story; a being called Shayde made contact with Mobius thanks to a temporary split in time and space. As soon as he touched Johnny, the hero was sent to the Shadow World and Shayde took on Johnny's identity. He and the other shadows are up to something, reveals Johnny, just as Sonic notices the other villains watching them. Back on Mobius, Shayde has revealed his plan to replace all of the heroes with evil doubles and take over the world. Shortfuse isn't so keen to go along with the plan and bursts out of his cage, his laser having been weakening the cell's bars all the time. In the Shadow Dimension, Sonic is trying to come up with a plan to solve things without touching anybody. The hedgehog spots two aliens guarding a room and a stupid enemy reveals that the Black Emerald is inside - the only thing that can destroy them.
Sonic leaps over the guards and attempts to destroy the Emerald, but is grabbed by one of the guards. Instantly, the villain turns into an exact copy of Sonic, albeit evil. The real Sonic decides to test the new Sonic's speed and punches the Black Emerald away. The double isn't fast enough and the Emerald shatters, condemning the Shadow Dimension to non-existance. The world begins to rip to pieces and Sonic and Johnny begin to fade away. Fortunately, Tekno has managed to find a way to reverse the matter transporter and summons the heroes home. An irate Shayde shoots at the heroes but misses, hitting his transporter. Johnny is furious and punches Shayde, causing the villain to return home. Tails suggests they all quickly leave since the transporter is about to blow. As they look upon the destruction of Robotnik's destroyed base, the heroes contemplate having seen the last of the shadows.
- Shayde/Agent X makes his final appearance.
- The original plan was that Johnny was Agent X and he betrayed Sonic to Robotnik. Robotnik was dropped because he was being used in the Drakon Empire stories, and he got cold feet over a real traitor when Nigel Kitching said he felt Johnny was "too nice a guy". "In retrospect, it weakens the impact of the end... I still think we should have had one long standing character turn traitor, not just for shock value, but to show what long term effects of being a freedom fighter could do to someone."
- Tails states that every Badnik on the planet must be here. However, not all Badniks can fly.
- The shadow that became Sonic only actually touched his shoe, suggesting he could have turned into some Power Sneakers...
- Sonic and Johnny's return to Mobius makes no sense. Since the matter transporter was reversed, Sonic should have reappeared in the matter transporter. Johnny didn't even travel using the transporter so the machine probably shouldn't have locked on to him.
- Then again, it may be that the process involved in bringing them back was more complicated than just reversing the equipment and Tekno just simplified the explanation to make it easier for everyone else to understand.
- Robotnik's base should be in the jungle of the Green Grove Zone but seems to be in a grassy field by the end of this story. Nevertheless, the base is now completely destroyed.
A wide variety of Badniks, old and new, were sent to attack Sonic and the gang:
As well as several designs first created on Flickies' Island.