Finally, Knuckles the Echidna has made it home to the Floating Island, armed with a chest full of documents obtained from Captain Plunder. His first stop is the Mushroom Hill Zone to check on the Emerald Hill folk, but things don't look good as he sees that the place is deserted, many doors and windows smashed. Hopping back on his pterodactyl, he heads off to the Emerald Chamber for more answers. In the shadows, a mysterious figure points his gun at Knuckles, but another voice warns him to wait, wanting to savour the moment. Inside, Knuckles gets ready to scan for life-signs, but his attention is turned by a shadow in the corner of the room, from somebody running away. Thinking the worst, Knuckles gives chase, demanding to know what happened to the Emerald Hill folk. Grabbing the assailant's leg before he turns the corner, Knuckles is shocked to find Porker Lewis. The terrified pig thought Knuckles was somebody else, someone who had come in the night and kidnapped all the villagers. Porker had escaped by navigating the island's tunnel system and had begun to set up communications to the Special Zone. Back in the Emerald Chamber, they see that Charmy Bee is on the screen, and Porker asks to speak to Sonic the Hedgehog. Once Sonic appears, Porker urgently asks for help, but the communicator is shot to bits, knocking Porker out. Knuckles turns to find Doctor Zachary, old foe Doctor Robotnik and three menacing Guardian Robots.
Knuckles and Porker are marched away by the robots that took the Emerald Hill folk away. Zachary reveals that he barely survived his previous fall from the Floating Island, having managed to manually pilot the robot that was falling with him. However, with the wing damaged, he was still left with horrendous injuries. Fortunately found by a Trooper patrol, Robotnik reveals that he was fascinated by the appearance of another echidna and rebuilt him with Badnik technology. In return, Zachary led Robotnik to the location of his greatest nuisances, the people of the Emerald Hill. The heroes are led to a new building, where Knuckles sees that all of the villagers have been strapped into some kind of machine. Robotnik states that they are about to become part of a Biological Computer, one that uses living brains instead of microchips. In the skies above, the Omni-Viewer watches on, horrified.
Porker and Knuckles find themselves strapped into the machine and Robotnik motions to pull the switch, dooming them forever. Knuckles manages to break out of his restraints just in time and destroys the master switch. Zachary orders the Guardian Robots to kill Knuckles while he gets the back-up switch ready. In mere minutes, the plan will be completed. Zachary reveals that, like Knuckles, he is an echidna and knows secrets of the island even its guardian doesn't know. Locating the hidden store of robots, all Zachary had to do was add some software of his own to make them his "unstoppable slaves". Unfortunately, as he was talking, Knuckles manages to break free from the robots. Leaping at Robotnik, Zachary defends his master by shooting his fellow echidna in the nick of time. With Knuckles groggy, Robotnik can finally get to work... but a third distraction occurs! Zachary looks to the sky quickly enough to see the Black Asteroid explode in the sky...
- Sonic's appearance on the computer and Omni's vision in the sky directly links with the events of Doomsday, the simultaneously-running Sonic story.