Dr. Robotnik built this device on the Floating Island after being informed by the malevolent echidna Doctor Zachary of the whereabouts of the Emerald Hill folk. Instead of microchips, the computer would use the living brains of Mobians for its processes. Once the computer was brought online, the victims installed on it could not be freed without being killed. Robotnik decided upon this fate as his revenge against Sonic and the Emerald Hill folk who were in hiding in the Mushroom Hill Zone. They were rounded up by Dr. Zachary who used modern software to take control of the Floating Island's Guardian Robots and capture them.
Knuckles the Echidna and Porker Lewis were also captured by Robotnik and Zachary and installed on the Biological Computer. Knuckles managed to escape from his restraints, however, and attempted to stop the two evil scientists. Thanks to Knuckles' interference, Robotnik failed to activate the computer before the Omni-Viewer transported the Black Asteroid from the Special Zone. When the asteroid exploded, the electromagnetic pulse that resulted shut down all electrical systems on Mobius, including the Bio-Computer, rendering it useless.
Sonic the Comic Online
A version of the biological computer would be seen in a later Sonic the Comic Online story, with Shortfuse the Cybernik apparently becoming evil once again. Controlled by someone else, Shorty constructed a computer and strapped his victims into it. However, it has been said by artist Chris G that this was just a tribute and wasn't really a biological computer. However, visually, it bears a striking resemblance.