The core program is a yellow energy core that controls the flow of data within cyberspace, and according to Black Doom, destroying it would stop such transmission of data throughout cyberspace, preventing the residents of earth to communicate or send information to one another. According to the Rouge the Bat, it is located in the "main room" of Digital Circuit.
In gameplay, the core program is encountered only in Digital Circuit. In the Dark mission for this Stage, the player has to find the core program and destroy it for the Black Arms in order to cripple their human enemies on earth.
- It is similar to Eden from Rez, another game published by Sega. In that game, after Swayzak the virus shuts down Eden, the residents of earth cannot communicate or send information to one another, just like what happens after Shadow deletes the core.